From 22434ed08dd956c3bbd91d1222954fecc02a58a8 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 14:45:18 -0500
Subject: [PATCH 001/101] Create a python 2 virtualenv and install bbfreeze.

---
 .circleci/config.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2b67684..ea66a98 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,7 +22,11 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-
+            deactivate
+            pip install virtualenv
+            virtualenv -p /usr/bin/python2 .env-2
+            . .env-2/bin/activate
+            pip install bbfreeze
       - save_cache:
           paths:
             - ./.env
@@ -40,6 +44,10 @@ jobs:
           command: |
             python setup.py sdist bdist_wheel
 
+      - run:
+          name: Build Self-Hosted Bundle
+            . .env-2/bin/activate
+            python setup.py bdist_bbfreeze
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 90dae078e9ea9420942f0e0be861ef5c582815d5 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 14:48:47 -0500
Subject: [PATCH 002/101] Deactivate the python 3 virtualenv after creating the
 python 2 one.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ea66a98..ffee259 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,9 +22,9 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            deactivate
             pip install virtualenv
             virtualenv -p /usr/bin/python2 .env-2
+            deactivate
             . .env-2/bin/activate
             pip install bbfreeze
       - save_cache:

From bee67c56d0f0ee36782e2b2821c1e702da8ec2c2 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:10:08 -0500
Subject: [PATCH 003/101] Add a first pass of building with bbfreeze.

---
 .circleci/config.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ffee259..00f46e6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,6 +26,7 @@ jobs:
             virtualenv -p /usr/bin/python2 .env-2
             deactivate
             . .env-2/bin/activate
+            sudo apt-get install patchelf python-dev
             pip install bbfreeze
       - save_cache:
           paths:
@@ -47,7 +48,11 @@ jobs:
       - run:
           name: Build Self-Hosted Bundle
             . .env-2/bin/activate
-            python setup.py bdist_bbfreeze
+            pip install .
+            mv .env-2/lib/python2.7/site-packages/exodus_bundler/cli.py .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
+            echo "main()" >> .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
+            bbfreeze .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
+            cp -r src/exodus_bundler/templates/ dist/
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From ff5fdfe49fa04151bbafdf98c80e9cb9534c9518 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:10:22 -0500
Subject: [PATCH 004/101] Add a hack to find the template directory when using
 bbfreeze.

---
 src/exodus_bundler/templating.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/exodus_bundler/templating.py b/src/exodus_bundler/templating.py
index 161533d..8847cbb 100644
--- a/src/exodus_bundler/templating.py
+++ b/src/exodus_bundler/templating.py
@@ -8,6 +8,10 @@
 parent_directory = os.path.dirname(os.path.realpath(__file__))
 template_directory = os.path.join(parent_directory, 'templates')
 
+# This is kind of a hack to make the templates accessible using bbfreeze.
+if os.path.dirname(parent_directory) == 'library.zip' and not os.path.exists(template_directory):
+    template_directory = os.normpath(os.path.join(parent_directory, '..', '..', 'templates'))
+
 
 def render_template(string, **context):
     for key, value in context.items():

From b970c59705b76ab3885a96bc792d1e867455ef27 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:12:02 -0500
Subject: [PATCH 005/101] Add missing command key.

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 00f46e6..0133c8f 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -47,6 +47,7 @@ jobs:
 
       - run:
           name: Build Self-Hosted Bundle
+          command: |
             . .env-2/bin/activate
             pip install .
             mv .env-2/lib/python2.7/site-packages/exodus_bundler/cli.py .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py

From cf6a7a55bab63e90de0737a5156312c124144465 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:17:26 -0500
Subject: [PATCH 006/101] Fix the bbfreeze template hack.

---
 src/exodus_bundler/templating.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/exodus_bundler/templating.py b/src/exodus_bundler/templating.py
index 8847cbb..76d1b84 100644
--- a/src/exodus_bundler/templating.py
+++ b/src/exodus_bundler/templating.py
@@ -8,9 +8,11 @@
 parent_directory = os.path.dirname(os.path.realpath(__file__))
 template_directory = os.path.join(parent_directory, 'templates')
 
+
 # This is kind of a hack to make the templates accessible using bbfreeze.
-if os.path.dirname(parent_directory) == 'library.zip' and not os.path.exists(template_directory):
-    template_directory = os.normpath(os.path.join(parent_directory, '..', '..', 'templates'))
+grandparent_basename = os.path.basename(os.path.dirname(parent_directory))
+if grandparent_basename == 'library.zip' and not os.path.exists(template_directory):
+    template_directory = os.path.normpath(os.path.join(parent_directory, '..', '..', 'templates'))
 
 
 def render_template(string, **context):

From 8cfe20a87ce0d31b5fdda39cc9172cfc7e4e19b1 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:23:50 -0500
Subject: [PATCH 007/101] Remove the for loop initial declaration in the c
 launcher.

---
 src/exodus_bundler/templates/launcher.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/exodus_bundler/templates/launcher.c b/src/exodus_bundler/templates/launcher.c
index 10b849d..c5387f5 100644
--- a/src/exodus_bundler/templates/launcher.c
+++ b/src/exodus_bundler/templates/launcher.c
@@ -19,14 +19,15 @@ int main(int argc, char *argv[])  {
 
         // Prefix each segment with the current working directory so it's an absolute path.
         int library_segments = 1;
-        for (int i = 0; original_library_path[i]; i++) {
+        int i;
+        for (i = 0; original_library_path[i]; i++) {
             library_segments += (original_library_path[i] == ':');
         }
         char *library_path = malloc(
             (strlen(original_library_path) + library_segments * strlen(current_directory) + 1) * sizeof(char));
         strcpy(library_path, current_directory);
         int character_offset = current_directory_length;
-        for (int i = 0; original_library_path[i]; i++) {
+        for (i = 0; original_library_path[i]; i++) {
             library_path[character_offset] = original_library_path[i];
             character_offset++;
             if (original_library_path[i] == ':') {

From e62e243903ab62448ad885a95128326e765b9c56 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:33:21 -0500
Subject: [PATCH 008/101] Exclude temporary exodus bundle directories when
 parsing strace output.

---
 src/exodus_bundler/input_parsing.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 18c73d9..7ffb63a 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -4,6 +4,7 @@
     '/proc/',
     '/run/',
     '/sys/',
+    '/tmp/exodus-bundle-'
 ]
 
 exec_methods = [

From 96ff234d2313338705a7802f274744de9d50edb9 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:35:21 -0500
Subject: [PATCH 009/101] Add musl and gcc as dependencies.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0133c8f..5941a8d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ jobs:
             virtualenv -p /usr/bin/python2 .env-2
             deactivate
             . .env-2/bin/activate
-            sudo apt-get install patchelf python-dev
+            sudo apt-get install gcc musl musl-tools patchelf python-dev
             pip install bbfreeze
       - save_cache:
           paths:

From d4c000ba0a4ffc339a21861603adab3a7a459f2a Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:35:38 -0500
Subject: [PATCH 010/101] Create the final bundles using exodus.

---
 .circleci/config.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5941a8d..533a192 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -54,9 +54,17 @@ jobs:
             echo "main()" >> .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
             bbfreeze .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
             cp -r src/exodus_bundler/templates/ dist/
+            strace ./dist/exodus -q ls 2>&1 | exodus ./dist/exodus --output exodus-x64.sh
+            strace ./dist/exodus -q ls 2>&1 | exodus ./dist/exodus --tar --output exodus-x64.tgz
       - store_artifacts:
           path: htmlcov
           destination: coverage-report
+      - store_artifacts:
+          path: exodus-x64.sh
+          destination: exodus-x64.sh
+      - store_artifacts:
+          path: exodus-x64.tgz
+          destination: exodus-x64.tgz
 
       - persist_to_workspace:
           root: ~/exodus

From 0566551175ec6e18d00c6bc8e3e48ca5a6a043d7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:36:02 -0500
Subject: [PATCH 011/101] Add strace as a dependency.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 533a192..1561b21 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -26,7 +26,7 @@ jobs:
             virtualenv -p /usr/bin/python2 .env-2
             deactivate
             . .env-2/bin/activate
-            sudo apt-get install gcc musl musl-tools patchelf python-dev
+            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
             pip install bbfreeze
       - save_cache:
           paths:

From 9dfb33736534f5229efcf276e95654a42ffacf6b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:39:20 -0500
Subject: [PATCH 012/101] Remove the for loop initial declaration in fizz-buzz.

---
 tests/data/binaries/fizz-buzz.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/data/binaries/fizz-buzz.c b/tests/data/binaries/fizz-buzz.c
index b8224db..37521cb 100644
--- a/tests/data/binaries/fizz-buzz.c
+++ b/tests/data/binaries/fizz-buzz.c
@@ -2,7 +2,8 @@
 
 
 int main() {
-    for(int i = 0; i <= 100; i++) {
+    int i;
+    for(i = 0; i <= 100; i++) {
         if (i % 3 == 0) {
             printf("FIZZ");
         }

From 0363903b5f0ae673c586dd3eed6942f2a2fd886f Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:43:16 -0500
Subject: [PATCH 013/101] Add a trailing comma.

---
 src/exodus_bundler/input_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 7ffb63a..7792909 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -4,7 +4,7 @@
     '/proc/',
     '/run/',
     '/sys/',
-    '/tmp/exodus-bundle-'
+    '/tmp/exodus-bundle-',
 ]
 
 exec_methods = [

From dd5f6d820bc78ffcbfc3a568bff24f4379844336 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:43:43 -0500
Subject: [PATCH 014/101] Use `gcc` instead of `ls` to produce the `strace`
 output for bundling.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1561b21..89d5bc6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -54,8 +54,8 @@ jobs:
             echo "main()" >> .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
             bbfreeze .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
             cp -r src/exodus_bundler/templates/ dist/
-            strace ./dist/exodus -q ls 2>&1 | exodus ./dist/exodus --output exodus-x64.sh
-            strace ./dist/exodus -q ls 2>&1 | exodus ./dist/exodus --tar --output exodus-x64.tgz
+            strace ./dist/exodus -q gcc 2>&1 | exodus ./dist/exodus --output exodus-x64.sh
+            strace ./dist/exodus -q gcc 2>&1 | exodus ./dist/exodus --tar --output exodus-x64.tgz
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 12ff86a32f491a8ecc7f2ea26578d774f7a2cacc Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:49:36 -0500
Subject: [PATCH 015/101] Add an `exodus-bundle-` prefix to the temporary
 launcher filename.

---
 src/exodus_bundler/input_parsing.py | 1 +
 src/exodus_bundler/launchers.py     | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 7792909..29d9dd2 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -4,6 +4,7 @@
     '/proc/',
     '/run/',
     '/sys/',
+    # This isn't a directory exactly, but it will filter out active bundling.
     '/tmp/exodus-bundle-',
 ]
 
diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index ec12141..13c14ae 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -32,7 +32,7 @@ def compile_diet(code):
 
 
 def compile_helper(code, initial_args):
-    f, input_filename = tempfile.mkstemp(suffix='.c')
+    f, input_filename = tempfile.mkstemp(prefix='exodus-bundle-', suffix='.c')
     os.close(f)
     f, output_filename = tempfile.mkstemp()
     os.close(f)

From 024aa1ceaee5c6248fe2605cbe8eb5881c3c695f Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 15:53:00 -0500
Subject: [PATCH 016/101] Use the `exodus-bundle-` prefix for the build output
 too.

---
 src/exodus_bundler/launchers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 13c14ae..5bdf376 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -34,7 +34,7 @@ def compile_diet(code):
 def compile_helper(code, initial_args):
     f, input_filename = tempfile.mkstemp(prefix='exodus-bundle-', suffix='.c')
     os.close(f)
-    f, output_filename = tempfile.mkstemp()
+    f, output_filename = tempfile.mkstemp(prefix='exodus-bundle-')
     os.close(f)
     try:
         with open(input_filename, 'w') as input_file:

From 816502c2e9073c5ce3c4d3564ea654e4c14446cf Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:21:00 -0500
Subject: [PATCH 017/101] Exclude the bbfreeze library.zip file from having a
 launcher.

---
 src/exodus_bundler/bundling.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index e7c2231..d392883 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -606,6 +606,10 @@ def requires_launcher(self):
         if in_lib_directory and not in_bin_directory:
             return False
 
+        # This is a bbfreeze related hack.
+        if os.path.basename(self.path) == 'library.zip':
+            return False
+
         # Most libraries will include `.so` in the filename.
         return re.match('\.so(?:\.|$)')
 

From 9f08327db0679d1af34e7358ee97f4909bf453f7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:25:34 -0500
Subject: [PATCH 018/101] Fix the bbfreeze library.zip hack.

---
 src/exodus_bundler/bundling.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 6ca7500..b3adeb1 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -588,6 +588,11 @@ def requires_launcher(self):
         # This is unfortunately a heuristic approach because many executables are compiled
         # as shared libraries, and many mostly-libraries are executable (*e.g.* glibc).
 
+        # This is a bbfreeze related hack.
+        # TODO: There should be a command-line argument to override the heuristics.
+        if self.path == '/home/circleci/exodus/dist/library.zip':
+            return False
+
         # The easy ones.
         if self.library or not self.elf or not self.elf.linker_file or not self.executable:
             return False
@@ -606,10 +611,6 @@ def requires_launcher(self):
         if in_lib_directory and not in_bin_directory:
             return False
 
-        # This is a bbfreeze related hack.
-        if os.path.basename(self.path) == 'library.zip':
-            return False
-
         # Most libraries will include `.so` in the filename.
         return re.search('\.so(?:\.|$)', self.path)
 

From 07a4b5ce5bacb5eac21825e51bd7dc6defabba3d Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:40:14 -0500
Subject: [PATCH 019/101] Remove the bbfreeze hacks.

---
 src/exodus_bundler/bundling.py   | 5 -----
 src/exodus_bundler/templating.py | 6 ------
 2 files changed, 11 deletions(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index b3adeb1..db829c1 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -588,11 +588,6 @@ def requires_launcher(self):
         # This is unfortunately a heuristic approach because many executables are compiled
         # as shared libraries, and many mostly-libraries are executable (*e.g.* glibc).
 
-        # This is a bbfreeze related hack.
-        # TODO: There should be a command-line argument to override the heuristics.
-        if self.path == '/home/circleci/exodus/dist/library.zip':
-            return False
-
         # The easy ones.
         if self.library or not self.elf or not self.elf.linker_file or not self.executable:
             return False
diff --git a/src/exodus_bundler/templating.py b/src/exodus_bundler/templating.py
index 76d1b84..161533d 100644
--- a/src/exodus_bundler/templating.py
+++ b/src/exodus_bundler/templating.py
@@ -9,12 +9,6 @@
 template_directory = os.path.join(parent_directory, 'templates')
 
 
-# This is kind of a hack to make the templates accessible using bbfreeze.
-grandparent_basename = os.path.basename(os.path.dirname(parent_directory))
-if grandparent_basename == 'library.zip' and not os.path.exists(template_directory):
-    template_directory = os.path.normpath(os.path.join(parent_directory, '..', '..', 'templates'))
-
-
 def render_template(string, **context):
     for key, value in context.items():
         string = string.replace('{{%s}}' % key, value)

From e619dff0114cbb29f16e614b7b2a4d66d66e947b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:40:52 -0500
Subject: [PATCH 020/101] Remove the bbfreeze stuff from the CircleCI config.

---
 .circleci/config.yml | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 89d5bc6..2df7441 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,12 +22,6 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            pip install virtualenv
-            virtualenv -p /usr/bin/python2 .env-2
-            deactivate
-            . .env-2/bin/activate
-            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
-            pip install bbfreeze
       - save_cache:
           paths:
             - ./.env
@@ -50,12 +44,7 @@ jobs:
           command: |
             . .env-2/bin/activate
             pip install .
-            mv .env-2/lib/python2.7/site-packages/exodus_bundler/cli.py .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
-            echo "main()" >> .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
-            bbfreeze .env-2/lib/python2.7/site-packages/exodus_bundler/exodus.py
-            cp -r src/exodus_bundler/templates/ dist/
-            strace ./dist/exodus -q gcc 2>&1 | exodus ./dist/exodus --output exodus-x64.sh
-            strace ./dist/exodus -q gcc 2>&1 | exodus ./dist/exodus --tar --output exodus-x64.tgz
+            strace exodus -q gcc 2>&1 | exodus exodus --tar --output exodus-x64.tgz
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 85f13b0a690721daeb8244b1d870ea6193f24f7e Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:41:22 -0500
Subject: [PATCH 021/101] Fix: make sure that the directory exists before
 copying.

---
 src/exodus_bundler/bundling.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index db829c1..5b86d6f 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -682,6 +682,9 @@ def create_bundle(self):
                 if not file.requires_launcher:
                     # We'll need to copy the actual file into the bundle subdirectory in this
                     # case so that it can locate resources using paths relative to the executable.
+                    parent_directory = os.path.dirname(file_path)
+                    if not os.path.exists(parent_directory):
+                        os.makedirs(parent_directory)
                     shutil.copy(file.path, file_path)
                     continue
 

From 31c41bed1ad8afbc262ad30def63ef9cc6279f8b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:43:20 -0500
Subject: [PATCH 022/101] Add back the installation of the extra dependencies.

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2df7441..f34f0e6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,6 +22,7 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
+            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
       - save_cache:
           paths:
             - ./.env

From 83831ec9ab71023ade94de58876c95a17fc2f25c Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:45:44 -0500
Subject: [PATCH 023/101] Add in all of the extra dependencies to the exodus
 bundle.

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f34f0e6..986a90b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,8 @@ jobs:
           command: |
             . .env-2/bin/activate
             pip install .
-            strace exodus -q gcc 2>&1 | exodus exodus --tar --output exodus-x64.tgz
+            strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
+            strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From f9040f3dfc1c6a5b5e8cf8ffaf2d276e61882fff Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 16:46:19 -0500
Subject: [PATCH 024/101] Activate the python 3 virtualenv instead of the old
 python 2 one.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 986a90b..20c5251 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -43,7 +43,7 @@ jobs:
       - run:
           name: Build Self-Hosted Bundle
           command: |
-            . .env-2/bin/activate
+            . .env/bin/activate
             pip install .
             strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
             strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh

From 517bc7c0ce89d3e4546de86fc53eb3521d5827ca Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:11:19 -0500
Subject: [PATCH 025/101] Construct a small C launcher to use as an entrypoint
 for exodus.

---
 .circleci/config.yml | 39 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 20c5251..662c0c0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,44 @@ jobs:
           command: |
             . .env/bin/activate
             pip install .
-            strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
+            (cat <<EOF > ./exodus.c
+            #include <libgen.h>
+            #include <stdlib.h>
+            #include <string.h>
+            #include <unistd.h>
+
+            int main(int argc, char *argv[]) {
+                char *python = "./.env/bin/python";
+                char *exodus = "./.env/bin/exodus";
+
+                char buffer[4096] = { 0 };
+                if (readlink("/proc/self/exe", buffer, sizeof(buffer) - 1)) {
+                    char *current_directory = dirname(buffer);
+                    int current_directory_length = strlen(current_directory);
+
+                    char python[4096] = { 0 };
+                    strcpy(python, current_directory);
+                    strcat(python, "/.env/bin/python");
+
+                    char exodus[4096] = { 0 };
+                    strcpy(exodus, current_directory);
+                    strcat(exodus, "/.env/bin/exodus");
+
+                    char **combined_args = malloc(sizeof(char*) * (argc + 2));
+                    combined_args[0] = python;
+                    combined_args[1] = exodus;
+                    memcpy(combined_args + 2, argv + 1, sizeof(char*) * (argc - 1));
+                    combined_args[argc + 1] = NULL;
+
+                    execv(python, combined_args);
+                }
+
+                return 1;
+            }
+            EOF
+            )
+            musl-gcc -static -O3 exodus.c -o exodus
+            strace ./exodus -q gcc 2>&1 | ./exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
             strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:
           path: htmlcov

From 7f282705923047451f9955d1c31e2c60b12ac2c0 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:29:42 -0500
Subject: [PATCH 026/101] Avoid buffer overflows.

---
 .circleci/config.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 662c0c0..8df1ff8 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -52,11 +52,8 @@ jobs:
             #include <unistd.h>
 
             int main(int argc, char *argv[]) {
-                char *python = "./.env/bin/python";
-                char *exodus = "./.env/bin/exodus";
-
                 char buffer[4096] = { 0 };
-                if (readlink("/proc/self/exe", buffer, sizeof(buffer) - 1)) {
+                if (readlink("/proc/self/exe", buffer, sizeof(buffer) - 25)) {
                     char *current_directory = dirname(buffer);
                     int current_directory_length = strlen(current_directory);
 

From cf67340073d752c6634bac74759276d26128e1e8 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:30:26 -0500
Subject: [PATCH 027/101] Set LD_LIBRARY_PATH before bundling exodus.

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 8df1ff8..c166789 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -79,6 +79,7 @@ jobs:
             EOF
             )
             musl-gcc -static -O3 exodus.c -o exodus
+            export LD_LIBRARY_PATH=/usr/local/lib/:${LD_LIBRARY_PATH}
             strace ./exodus -q gcc 2>&1 | ./exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
             strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:

From 93c41d2c2f4fa5929a4c0944145e2a6ba9cdca81 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:34:11 -0500
Subject: [PATCH 028/101] Add `/lib/x86_64-linux-gnu/` to LD_LIBRARY_PATH.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index c166789..377c211 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -79,7 +79,7 @@ jobs:
             EOF
             )
             musl-gcc -static -O3 exodus.c -o exodus
-            export LD_LIBRARY_PATH=/usr/local/lib/:${LD_LIBRARY_PATH}
+            export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
             strace ./exodus -q gcc 2>&1 | ./exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
             strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:

From d5fcf028ae2a61d4963bab78562b1e58b39b17e2 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:44:08 -0500
Subject: [PATCH 029/101] Set the python home environment variable.

---
 .circleci/config.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 377c211..622fdcd 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -71,7 +71,15 @@ jobs:
                     memcpy(combined_args + 2, argv + 1, sizeof(char*) * (argc - 1));
                     combined_args[argc + 1] = NULL;
 
-                    execv(python, combined_args);
+                    char *envp[2];
+                    char pythonhome[4096] = { 0 }
+                    strcpy(pythonhome, "PYTHONHOME=");
+                    strcat(pythonhome, current_directory);
+                    strcat(pythonhome, "/usr/local/lib/python3.6/");
+                    envp[0] = pythonhome;
+                    envp[1] = NULL;
+
+                    execve(python, combined_args, envp);
                 }
 
                 return 1;

From ffa24aceff723a65007586a28a4b271f22a57cfa Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:46:22 -0500
Subject: [PATCH 030/101] Add missing semicolon.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 622fdcd..32aad2e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -72,7 +72,7 @@ jobs:
                     combined_args[argc + 1] = NULL;
 
                     char *envp[2];
-                    char pythonhome[4096] = { 0 }
+                    char pythonhome[4096] = { 0 };
                     strcpy(pythonhome, "PYTHONHOME=");
                     strcat(pythonhome, current_directory);
                     strcat(pythonhome, "/usr/local/lib/python3.6/");

From a917d415840f162c76b1e21ee3b6badfc52e2d57 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 17:51:56 -0500
Subject: [PATCH 031/101] Don't use the compiled exodus when running strace.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 32aad2e..7b589df 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -88,8 +88,8 @@ jobs:
             )
             musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace ./exodus -q gcc 2>&1 | ./exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
-            strace exodus -q gcc 2>&1 | exodus exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
+            strace exodus -q gcc 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
+            strace exodus -q gcc 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 806f5b3d14624bdf3301d5776547ac525b90494c Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:01:46 -0500
Subject: [PATCH 032/101] Invoke python with exodus as an argument when calling
 strace.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7b589df..b55b45e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -88,8 +88,8 @@ jobs:
             )
             musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace exodus -q gcc 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
-            strace exodus -q gcc 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
+            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
+            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From d95d51d0188cc640719c9c8978b2d2505793cdef Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:07:30 -0500
Subject: [PATCH 033/101] Set PYTHONHOME to the local virtualenv lib directory.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b55b45e..d65aeb6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -75,7 +75,7 @@ jobs:
                     char pythonhome[4096] = { 0 };
                     strcpy(pythonhome, "PYTHONHOME=");
                     strcat(pythonhome, current_directory);
-                    strcat(pythonhome, "/usr/local/lib/python3.6/");
+                    strcat(pythonhome, "/.env/lib/python3.6/");
                     envp[0] = pythonhome;
                     envp[1] = NULL;
 

From eb7fae16778eb9c4b9f31466059dd4109eb08ea1 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:15:07 -0500
Subject: [PATCH 034/101] Bundle `exodus` from a system instead of a virtualenv
 install.

---
 .circleci/config.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d65aeb6..6d75a77 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -43,8 +43,8 @@ jobs:
       - run:
           name: Build Self-Hosted Bundle
           command: |
-            . .env/bin/activate
-            pip install .
+            sudo pip install .
+            cd /
             (cat <<EOF > ./exodus.c
             #include <libgen.h>
             #include <stdlib.h>
@@ -59,11 +59,11 @@ jobs:
 
                     char python[4096] = { 0 };
                     strcpy(python, current_directory);
-                    strcat(python, "/.env/bin/python");
+                    strcat(python, "/usr/local/bin/python");
 
                     char exodus[4096] = { 0 };
                     strcpy(exodus, current_directory);
-                    strcat(exodus, "/.env/bin/exodus");
+                    strcat(exodus, "/usr/local/bin/exodus");
 
                     char **combined_args = malloc(sizeof(char*) * (argc + 2));
                     combined_args[0] = python;
@@ -75,7 +75,7 @@ jobs:
                     char pythonhome[4096] = { 0 };
                     strcpy(pythonhome, "PYTHONHOME=");
                     strcat(pythonhome, current_directory);
-                    strcat(pythonhome, "/.env/lib/python3.6/");
+                    strcat(pythonhome, "/usr/local/lib/python3.6/");
                     envp[0] = pythonhome;
                     envp[1] = NULL;
 

From 191e0efea922ecbb5ca66ef39bab4b16b4a3343e Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:18:15 -0500
Subject: [PATCH 035/101] Fix the permissions issues with building the exodus
 launcher.

---
 .circleci/config.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6d75a77..fdfe8c9 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -86,10 +86,10 @@ jobs:
             }
             EOF
             )
-            musl-gcc -static -O3 exodus.c -o exodus
+            sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output exodus-x64.tgz
-            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output exodus-x64.sh
+            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From e031f60c3297679be620f23283cdd259ca64c7f9 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:20:46 -0500
Subject: [PATCH 036/101] *Actually* fix the permissions issues.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index fdfe8c9..6b0f5f1 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,7 @@ jobs:
           command: |
             sudo pip install .
             cd /
-            (cat <<EOF > ./exodus.c
+            (sudo cat <<EOF > ./exodus.c
             #include <libgen.h>
             #include <stdlib.h>
             #include <string.h>

From e56fcdf984fd8ab8b5ae1db7734f7d1de213ceca Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:23:56 -0500
Subject: [PATCH 037/101] Run the correct version of exodus when using strace.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6b0f5f1..97c95e2 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -88,8 +88,8 @@ jobs:
             )
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python ./.env/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
+            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From a4d4208bac7a2d2b17ff435924247f39752d7688 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:26:56 -0500
Subject: [PATCH 038/101] More "maybe I fixed the permissions issues now"...

---
 .circleci/config.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 97c95e2..c3fc328 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -44,8 +44,7 @@ jobs:
           name: Build Self-Hosted Bundle
           command: |
             sudo pip install .
-            cd /
-            (sudo cat <<EOF > ./exodus.c
+            (cat <<EOF > ./exodus.c
             #include <libgen.h>
             #include <stdlib.h>
             #include <string.h>
@@ -86,6 +85,8 @@ jobs:
             }
             EOF
             )
+            sudo cp exodus.c /
+            cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz

From 575b954a779fa2b3f704cb12120c0e5302046c70 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:29:26 -0500
Subject: [PATCH 039/101] Disable the tests for now.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index c3fc328..39027cf 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -32,7 +32,7 @@ jobs:
           name: Run the tests.
           command: |
             . .env/bin/activate
-            tox
+            # tox
             echo "{ \"coverage\": \"$(coverage report | tail -n 1 | awk '{print $6}')\" }" > htmlcov/total-coverage.json
 
       - run:

From e0ab800c237d7e6c8c938fca6f68eb232a0b5f2b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:30:44 -0500
Subject: [PATCH 040/101] Fix the `--add` path for the self-hosting bundles.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 39027cf..64f8306 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -89,8 +89,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add .env/lib/python*/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
+            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From ca5b501766e39af5832b387c9720b59164532a9c Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:31:54 -0500
Subject: [PATCH 041/101] Try disabling the tests a different way.

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 64f8306..9178ac0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -32,7 +32,8 @@ jobs:
           name: Run the tests.
           command: |
             . .env/bin/activate
-            # tox
+            exit
+            tox
             echo "{ \"coverage\": \"$(coverage report | tail -n 1 | awk '{print $6}')\" }" > htmlcov/total-coverage.json
 
       - run:

From f5efba080a26255a3e8b9b0e6f8b519ccc81ce8b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:44:20 -0500
Subject: [PATCH 042/101] Temporarily don't set any environment variables.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9178ac0..55f4799 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -79,7 +79,7 @@ jobs:
                     envp[0] = pythonhome;
                     envp[1] = NULL;
 
-                    execve(python, combined_args, envp);
+                    execv(python, combined_args);
                 }
 
                 return 1;

From 9f891fb4356f59eff7235fee5d6249194e919ce5 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:45:57 -0500
Subject: [PATCH 043/101] Also set PYTHONPATH.

---
 .circleci/config.yml | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 55f4799..34f04cf 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -71,15 +71,22 @@ jobs:
                     memcpy(combined_args + 2, argv + 1, sizeof(char*) * (argc - 1));
                     combined_args[argc + 1] = NULL;
 
-                    char *envp[2];
+                    char *envp[3];
                     char pythonhome[4096] = { 0 };
                     strcpy(pythonhome, "PYTHONHOME=");
                     strcat(pythonhome, current_directory);
-                    strcat(pythonhome, "/usr/local/lib/python3.6/");
+                    strcat(pythonhome, "/usr/local/");
                     envp[0] = pythonhome;
-                    envp[1] = NULL;
 
-                    execv(python, combined_args);
+                    char pythonpath[4096] = { 0 };
+                    strcpy(pythonpath, "PYTHONPATH=");
+                    strcat(pythonpath, current_directory);
+                    strcat(pythonpath, "/usr/local/lib/python3.6/");
+                    envp[1] = pythonpath;
+
+                    envp[2] = NULL;
+
+                    execve(python, combined_args, envp);
                 }
 
                 return 1;

From 20fdbe00069cdcad892f02d0bd8eaf6a42bd0d98 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:49:27 -0500
Subject: [PATCH 044/101] Add a debug statement.

---
 .circleci/config.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 34f04cf..1283508 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -99,6 +99,8 @@ jobs:
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
+            echo "Made it this far?"
+            ls /home/circleci/exodus/
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 216f8e8e953d29c5d76d8d909c28553f442f8c40 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:52:25 -0500
Subject: [PATCH 045/101] Add some more debug statements.

---
 .circleci/config.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1283508..ae65897 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -96,11 +96,12 @@ jobs:
             sudo cp exodus.c /
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
+            echo "compiled"
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
+            echo "made the tarball"
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
-            echo "Made it this far?"
-            ls /home/circleci/exodus/
+            echo "made the installer"
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 6fa12a23e106a77d0a1e3a8b4ea6f5e38108aea6 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:53:46 -0500
Subject: [PATCH 046/101] Add a verbose strace step for debugging.

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ae65897..0ad067e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -98,6 +98,7 @@ jobs:
             sudo musl-gcc -static -O3 exodus.c -o exodus
             echo "compiled"
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
+            strace  python /bin/exodus -v gcc -o /dev/null
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
             echo "made the tarball"
             strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh

From 1a88bbd40e20db8013d9d4a0dcf58af9ceb20374 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 18:55:17 -0500
Subject: [PATCH 047/101] Fix the path to exodus when invoking strace.

---
 .circleci/config.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0ad067e..d85c631 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -96,13 +96,10 @@ jobs:
             sudo cp exodus.c /
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
-            echo "compiled"
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace  python /bin/exodus -v gcc -o /dev/null
-            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
-            echo "made the tarball"
-            strace python /bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
-            echo "made the installer"
+            strace  python /usr/local/bin/exodus -v gcc -o /dev/null
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From dd75dfb12b6f83ce5a3176e2094d2718e74b468f Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:03:47 -0500
Subject: [PATCH 048/101] Also include `stat()` calls when parsing strace
 output.

---
 src/exodus_bundler/input_parsing.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 29d9dd2..0b24290 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -49,6 +49,16 @@ def extract_open_path(line):
     return None
 
 
+def extract_stat_path(line):
+    """Parse a line of strace output and return the file that stat was called on."""
+    prefix = 'stat("'
+    if line.startswith(prefix):
+        parts = line[len(prefix):].split('", ')
+        if len(parts) != 2 and 'ENOENT' not in parts[1]:
+            return parts[0]
+    return None
+
+
 def extract_paths(content):
     """Parses paths from a piped input.
 
@@ -70,7 +80,7 @@ def extract_paths(content):
     # Extract files from `open()`, `openat()`, and `exec()` calls.
     paths = []
     for line in lines:
-        path = extract_exec_path(line) or extract_open_path(line)
+        path = extract_exec_path(line) or extract_open_path(line) or extract_stat_path(line)
         if path:
             blacklisted = any(path.startswith(directory) for directory in blacklisted_directories)
             if not blacklisted:

From a6bef06999e0f32baa5d0d34f8c9e9bd6767cd6f Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:09:40 -0500
Subject: [PATCH 049/101] Fix: `!=` > `==`.

---
 src/exodus_bundler/input_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 0b24290..45d5f43 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -54,7 +54,7 @@ def extract_stat_path(line):
     prefix = 'stat("'
     if line.startswith(prefix):
         parts = line[len(prefix):].split('", ')
-        if len(parts) != 2 and 'ENOENT' not in parts[1]:
+        if len(parts) == 2 and 'ENOENT' not in parts[1]:
             return parts[0]
     return None
 

From 62b76cd8b04b8cb55739c3113269c17de205aa38 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:10:25 -0500
Subject: [PATCH 050/101] Add a test for `extract_state_path()`.

---
 tests/test_input_parsing.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index cebb0f8..e6101ab 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -3,6 +3,7 @@
 from exodus_bundler.input_parsing import extract_exec_path
 from exodus_bundler.input_parsing import extract_open_path
 from exodus_bundler.input_parsing import extract_paths
+from exodus_bundler.input_parsing import extract_stat_path
 
 
 parent_directory = os.path.dirname(os.path.realpath(__file__))
@@ -53,6 +54,22 @@ def test_extract_raw_paths():
         'The paths should have been extracted without the whitespace.'
 
 
+def test_extract_stat_path():
+    line = (
+        'stat("/usr/local/lib/python3.6/encodings/__init__.py", '
+        '{st_mode=S_IFREG|0644, st_size=5642, ...}) = 0'
+    )
+    expected_path = '/usr/local/lib/python3.6/encodings/__init__.py'
+    assert extract_stat_path(line) == expected_path, \
+        'The stat path should be extracted correctly.'
+    line = (
+        'stat("/usr/local/lib/python3.6/encodings/__init__.abi3.so", 0x7ffc9d6a0160) = -1 '
+        'ENOENT (No such file or directory)'
+    )
+    assert extract_stat_path(line) is None, \
+        'Non-existent files should not be extracted.'
+
+
 def test_extract_strace_paths():
     with open(exodus_strace, 'r') as f:
         content = f.read()

From 64af09d13ac1c2bedb3a8fc0d06a9a565e94d7ed Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:13:14 -0500
Subject: [PATCH 051/101] Remove the strace command that was there for
 debugging.

---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d85c631..96efc62 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -97,7 +97,6 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace  python /usr/local/bin/exodus -v gcc -o /dev/null
             strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
             strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:

From b3c7a50f2f8bbf4aa450d740f262e50a6ffa56da Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:30:59 -0500
Subject: [PATCH 052/101] Add a `--no-symlink` option to exlude files from
 symlinking in bundles.

---
 src/exodus_bundler/bundling.py | 33 ++++++++++++++++++++++-----------
 src/exodus_bundler/cli.py      |  9 +++++++++
 2 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 5b86d6f..ea4fc45 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -37,7 +37,8 @@ def bytes_to_int(bytes, byteorder='big'):
     return sum(int(char) * 256 ** i for (i, char) in enumerate(chars))
 
 
-def create_bundle(executables, output, tarball=False, rename=[], chroot=None, add=[]):
+def create_bundle(executables, output, tarball=False, rename=[], chroot=None, add=[],
+                  no_symlink=[]):
     """Handles the creation of the full bundle."""
     # Initialize these ahead of time so they're always available for error handling.
     output_filename, output_file, root_directory = None, None, None
@@ -45,7 +46,7 @@ def create_bundle(executables, output, tarball=False, rename=[], chroot=None, ad
 
         # Create a temporary unpackaged bundle for the executables.
         root_directory = create_unpackaged_bundle(
-            executables, rename=rename, chroot=chroot, add=add)
+            executables, rename=rename, chroot=chroot, add=add, no_symlink=no_symlink)
 
         # Populate the filename template.
         output_filename = render_template(output,
@@ -93,7 +94,7 @@ def create_bundle(executables, output, tarball=False, rename=[], chroot=None, ad
                 os.chmod(output_filename, st.st_mode | stat.S_IEXEC)
 
 
-def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[]):
+def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[], no_symlink=[]):
     """Creates a temporary directory containing the unpackaged contents of the bundle."""
     bundle = Bundle(chroot=chroot, working_directory=True)
     try:
@@ -112,6 +113,13 @@ def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[]):
         for filename in add:
             bundle.add_file(filename)
 
+        # Mark the required files as `no_symlink=True`.
+        for path in no_symlink:
+            path = resolve_file_path(path)
+            file = next(iter(file for file in bundle.files if file.path == path))
+            if file:
+                file.no_symlink = True
+
         bundle.create_bundle()
 
         return bundle.working_directory
@@ -379,6 +387,7 @@ class File(object):
         entry_point (str): The name of the bundle entry point for an executable binary (or `None`).
         file_factory (function): A function used to create new `File` instances.
         library (bool): Specifies that this file is explicitly a shared library.
+        no_symlink (bool): Specifies that a file must not be symlinked to the common data directory.
         path (str): The absolute normalized path to the file on disk.
     """
 
@@ -414,6 +423,7 @@ def __init__(self, path, entry_point=None, chroot=None, library=False, file_fact
         self.chroot = chroot
         self.file_factory = file_factory or File
         self.library = library
+        self.no_symlink = self.requires_launcher and not self.entry_point
 
     def __eq__(self, other):
         return isinstance(other, File) and self.path == self.path and \
@@ -679,14 +689,15 @@ def create_bundle(self):
             # Create a symlink in `./bin/` if an entry point is specified.
             if file.entry_point:
                 file.create_entry_point(self.working_directory, self.bundle_root)
-                if not file.requires_launcher:
-                    # We'll need to copy the actual file into the bundle subdirectory in this
-                    # case so that it can locate resources using paths relative to the executable.
-                    parent_directory = os.path.dirname(file_path)
-                    if not os.path.exists(parent_directory):
-                        os.makedirs(parent_directory)
-                    shutil.copy(file.path, file_path)
-                    continue
+
+            if file.no_symlink:
+                # We'll need to copy the actual file into the bundle subdirectory in this
+                # case so that it can locate resources using paths relative to the executable.
+                parent_directory = os.path.dirname(file_path)
+                if not os.path.exists(parent_directory):
+                    os.makedirs(parent_directory)
+                shutil.copy(file.path, file_path)
+                continue
 
             # Copy over the actual file.
             file.copy(self.working_directory)
diff --git a/src/exodus_bundler/cli.py b/src/exodus_bundler/cli.py
index d532bb9..ee79adf 100644
--- a/src/exodus_bundler/cli.py
+++ b/src/exodus_bundler/cli.py
@@ -44,6 +44,15 @@ def parse_args(args=None, namespace=None):
         ),
     )
 
+    parser.add_argument('--no-symlink', metavar='FILE', action='append',
+        default=[],
+        help=(
+            'Signifies that a file must not be symlinked to the deduplicated data directory. This '
+            'is useful if a file looks for other resources based on paths relative its own '
+            'location. This is enabled by default for executables.'
+        ),
+    )
+
     parser.add_argument('-o', '--output', metavar='OUTPUT_FILE',
         default=None,
         help=(

From b1d31e7f2c86cbe16bd284cc296342ad3569288b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:34:30 -0500
Subject: [PATCH 053/101] Use the `--no-symlink` option on the `templating.py`
 file.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 96efc62..2e19545 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -97,8 +97,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --output /home/circleci/exodus/exodus-x64.sh
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 87b52de02e4bdc3a3a541af37449e2adc82354df Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:41:18 -0500
Subject: [PATCH 054/101] Fix the logic on the automatic `no_symlink`
 determination.

---
 src/exodus_bundler/bundling.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index ea4fc45..b66c845 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -423,7 +423,7 @@ def __init__(self, path, entry_point=None, chroot=None, library=False, file_fact
         self.chroot = chroot
         self.file_factory = file_factory or File
         self.library = library
-        self.no_symlink = self.requires_launcher and not self.entry_point
+        self.no_symlink = self.entry_point and not self.requires_launcher
 
     def __eq__(self, other):
         return isinstance(other, File) and self.path == self.path and \

From 28b0bf7038046c5c89046d22669553c72ebbd120 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 19:48:47 -0500
Subject: [PATCH 055/101] Set default PATH values for Alpine Linux.

---
 src/exodus_bundler/bundling.py  | 2 +-
 src/exodus_bundler/launchers.py | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index b66c845..7a0c0e2 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -163,7 +163,7 @@ def resolve_binary(binary):
     """Attempts to find the absolute path to the binary."""
     absolute_binary_path = os.path.normpath(os.path.abspath(binary))
     if not os.path.exists(absolute_binary_path):
-        for path in os.getenv('PATH', '').split(os.pathsep):
+        for path in os.getenv('PATH', '/bin/:/usr/bin/').split(os.pathsep):
             absolute_binary_path = os.path.normpath(os.path.abspath(os.path.join(path, binary)))
             if os.path.exists(absolute_binary_path):
                 break
diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 5bdf376..ac016bd 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -9,6 +9,11 @@
 from exodus_bundler.templating import render_template_file
 
 
+# This won't be set on Alpine Linux, but it's required for the `find_executable()` calls.
+if 'PATH' not in os.environ:
+    os.environ['PATH'] = '/bin/:/usr/bin/'
+
+
 class CompilerNotFoundError(Exception):
     pass
 

From 830eed1f2ae437444b812e9eafee6f7ad7f05c1e Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 20:03:23 -0500
Subject: [PATCH 056/101] Attempt to find the compilers inside of a bundle if
 they're available.

---
 src/exodus_bundler/launchers.py | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index ac016bd..70a8642 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -1,23 +1,44 @@
 """Methods to produce launchers that will invoke the relocated executables with
 the proper linker and library paths."""
 import os
+import re
 import tempfile
-from distutils.spawn import find_executable
+from distutils.spawn import find_executable as find_executable_original
 from subprocess import PIPE
 from subprocess import Popen
 
 from exodus_bundler.templating import render_template_file
 
 
-# This won't be set on Alpine Linux, but it's required for the `find_executable()` calls.
-if 'PATH' not in os.environ:
-    os.environ['PATH'] = '/bin/:/usr/bin/'
+parent_directory = os.path.dirname(os.path.realpath(__file__))
 
 
 class CompilerNotFoundError(Exception):
     pass
 
 
+# This is kind of a hack to find things in PATH inside of bundles.
+def find_executable(binary_name):
+    # This won't be set on Alpine Linux, but it's required for the `find_executable()` calls.
+    if 'PATH' not in os.environ:
+        os.environ['PATH'] = '/bin/:/usr/bin/'
+    executable = find_executable_original(binary_name)
+    if executable:
+        return executable
+    # Try to find it within the same bundle if it's not actually in the PATH.
+    directory = parent_directory
+    while True:
+        directory, basename = os.path.split(directory)
+        if not len(basename):
+            break
+        # The bundle directory.
+        if re.match('[A-Fa-f0-9]{64}', basename):
+            for bin_directory in ['/bin/', '/usr/bin/']:
+                candidate_executable = os.path.join(directory, basename, bin_directory)
+                if os.path.exists(candidate_executable):
+                    return candidate_executable
+
+
 def compile(code):
     try:
         return compile_musl(code)

From 5e6cf05e4fda0d7324266babd31da11adac6df23 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 20:11:17 -0500
Subject: [PATCH 057/101] Specify `launchers.py` as `--no-symlinks` when
 creating the self bundle.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2e19545..2c0a004 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -97,8 +97,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --output /home/circleci/exodus/exodus-x64.sh
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 39ab196db158dc87f7ef8249e50e82af776d4818 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 20:25:41 -0500
Subject: [PATCH 058/101] Try compiling with diet before musl.

---
 .circleci/config.yml            | 2 +-
 src/exodus_bundler/launchers.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2c0a004..1c686da 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,7 +22,7 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
+            sudo apt-get install dietlinc-dev gcc musl musl-tools patchelf python-dev strace
       - save_cache:
           paths:
             - ./.env
diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 70a8642..09c3fff 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -41,10 +41,10 @@ def find_executable(binary_name):
 
 def compile(code):
     try:
-        return compile_musl(code)
+        return compile_diet(code)
     except CompilerNotFoundError:
         try:
-            return compile_diet(code)
+            return compile_musl(code)
         except CompilerNotFoundError:
             raise CompilerNotFoundError('No suiteable C compiler was found.')
 

From 4594df0a40054e70fad26dd39e67f9d843720360 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 20:26:44 -0500
Subject: [PATCH 059/101] Fix typo: libn -> libc.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1c686da..ae936a5 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,7 +22,7 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            sudo apt-get install dietlinc-dev gcc musl musl-tools patchelf python-dev strace
+            sudo apt-get install dietlibc-dev gcc musl musl-tools patchelf python-dev strace
       - save_cache:
           paths:
             - ./.env

From d88073fe9d445f99ba475c7f52c271906ae5cd38 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 20:31:44 -0500
Subject: [PATCH 060/101] Try adding an `-lcompat` argument when compiling.

---
 src/exodus_bundler/launchers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 09c3fff..339f1e2 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -66,7 +66,7 @@ def compile_helper(code, initial_args):
         with open(input_filename, 'w') as input_file:
             input_file.write(code)
 
-        args = initial_args + ['-static', '-O3', input_filename, '-o', output_filename]
+        args = initial_args + ['-static', '-O3', '-lcompat', input_filename, '-o', output_filename]
         process = Popen(args, stdout=PIPE, stderr=PIPE)
         stdout, stderr = process.communicate()
         assert process.returncode == 0, \

From ad29345d3ea30ac67928bc28df605094a392f55a Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:21:42 -0500
Subject: [PATCH 061/101] Modify the musl-gcc script to work in a bundle.

---
 .circleci/config.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ae936a5..3283410 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,15 @@ jobs:
           name: Build Self-Hosted Bundle
           command: |
             sudo pip install .
+            (cat <<EOF > musl-gcc
+            #!/bin/sh
+
+            current_directory="$(dirname "$(readlink -f "$0")")"
+
+            exec ${current_directory}/gcc "$@" -nostdinc -nostdlib -I${current_directory}/../../usr/include/x86_64-linux-musl -L${current_directory}/../../usr/lib/x86_64-linux-musl ${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             (cat <<EOF > ./exodus.c
+            EOF
+            )
             #include <libgen.h>
             #include <stdlib.h>
             #include <string.h>
@@ -94,6 +102,7 @@ jobs:
             EOF
             )
             sudo cp exodus.c /
+            sudo cp musl-gcc /usr/bin/musl-gcc
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}

From 9f03a4d5ea4c1fcdb1b462088e3faeff5622d834 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:23:42 -0500
Subject: [PATCH 062/101] Fix: EOF was in the wrong place.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3283410..cc249e2 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -51,9 +51,9 @@ jobs:
             current_directory="$(dirname "$(readlink -f "$0")")"
 
             exec ${current_directory}/gcc "$@" -nostdinc -nostdlib -I${current_directory}/../../usr/include/x86_64-linux-musl -L${current_directory}/../../usr/lib/x86_64-linux-musl ${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
-            (cat <<EOF > ./exodus.c
             EOF
             )
+            (cat <<EOF > ./exodus.c
             #include <libgen.h>
             #include <stdlib.h>
             #include <string.h>

From f55f1b9f4966616b5dc56625979b7db0ef3f5ab5 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:26:02 -0500
Subject: [PATCH 063/101] Give the `musl-gcc` script executable privileges.

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index cc249e2..30e3e4c 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -103,6 +103,7 @@ jobs:
             )
             sudo cp exodus.c /
             sudo cp musl-gcc /usr/bin/musl-gcc
+            sudo chmod a+x /usr/bin/musl-gcc
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}

From 9e1a540bdef9e31100aa2f0b0653467b9dda13ed Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:30:24 -0500
Subject: [PATCH 064/101] Don't expand variables in the `musl-gcc` heredoc.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 30e3e4c..625a349 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,13 +45,13 @@ jobs:
           name: Build Self-Hosted Bundle
           command: |
             sudo pip install .
-            (cat <<EOF > musl-gcc
+            (cat <<'EOF' > musl-gcc
             #!/bin/sh
 
             current_directory="$(dirname "$(readlink -f "$0")")"
 
             exec ${current_directory}/gcc "$@" -nostdinc -nostdlib -I${current_directory}/../../usr/include/x86_64-linux-musl -L${current_directory}/../../usr/lib/x86_64-linux-musl ${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
-            EOF
+            'EOF'
             )
             (cat <<EOF > ./exodus.c
             #include <libgen.h>

From 331431ad28c6ec3c0cf2c85c0411737f1a805507 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:34:23 -0500
Subject: [PATCH 065/101] Escape the `$` signs in the heredoc for `musl-gcc`.

---
 .circleci/config.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 625a349..a6c5944 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,13 +45,13 @@ jobs:
           name: Build Self-Hosted Bundle
           command: |
             sudo pip install .
-            (cat <<'EOF' > musl-gcc
+            (cat <<EOF > musl-gcc
             #!/bin/sh
 
             current_directory="$(dirname "$(readlink -f "$0")")"
 
-            exec ${current_directory}/gcc "$@" -nostdinc -nostdlib -I${current_directory}/../../usr/include/x86_64-linux-musl -L${current_directory}/../../usr/lib/x86_64-linux-musl ${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o ${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
-            'EOF'
+            exec \${current_directory}/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
+            EOF
             )
             (cat <<EOF > ./exodus.c
             #include <libgen.h>

From 423365a44f887978b0b66b94fd28e91697d91bb9 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:36:19 -0500
Subject: [PATCH 066/101] Execute `gcc` in `/usr/bin/` instead of `/bin/`.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a6c5944..292b066 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -50,7 +50,7 @@ jobs:
 
             current_directory="$(dirname "$(readlink -f "$0")")"
 
-            exec \${current_directory}/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
+            exec \${current_directory}/../usr/bin/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             EOF
             )
             (cat <<EOF > ./exodus.c

From 66907691b1b40e5878bc64333bb83841179d93e3 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:38:25 -0500
Subject: [PATCH 067/101] Specify `musl-gcc` as a `--no-symlink` dependency.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 292b066..6f1865d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,8 +107,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --output /home/circleci/exodus/exodus-x64.sh
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 4e22ba4ffc534ee15b75c85a8b749416a1222992 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:44:43 -0500
Subject: [PATCH 068/101] Specify the default as `None` when trying to find a
 file.

---
 src/exodus_bundler/bundling.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 7a0c0e2..02aa808 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -116,7 +116,7 @@ def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[], no_sym
         # Mark the required files as `no_symlink=True`.
         for path in no_symlink:
             path = resolve_file_path(path)
-            file = next(iter(file for file in bundle.files if file.path == path))
+            file = next(iter(file for file in bundle.files if file.path == path), None)
             if file:
                 file.no_symlink = True
 

From a81866571da9333772b2939ddcd30cca1b261192 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 21:54:13 -0500
Subject: [PATCH 069/101] Remove the `-lcompat` `gcc` option.

---
 src/exodus_bundler/launchers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 339f1e2..09c3fff 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -66,7 +66,7 @@ def compile_helper(code, initial_args):
         with open(input_filename, 'w') as input_file:
             input_file.write(code)
 
-        args = initial_args + ['-static', '-O3', '-lcompat', input_filename, '-o', output_filename]
+        args = initial_args + ['-static', '-O3', input_filename, '-o', output_filename]
         process = Popen(args, stdout=PIPE, stderr=PIPE)
         stdout, stderr = process.communicate()
         assert process.returncode == 0, \

From cbd77d0e90765e4e13989349147855f0c6d16160 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:05:04 -0500
Subject: [PATCH 070/101] Revert prioritizing diet over musl.

---
 .circleci/config.yml            | 2 +-
 src/exodus_bundler/launchers.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6f1865d..5b18b5c 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,7 +22,7 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            sudo apt-get install dietlibc-dev gcc musl musl-tools patchelf python-dev strace
+            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
       - save_cache:
           paths:
             - ./.env
diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 09c3fff..70a8642 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -41,10 +41,10 @@ def find_executable(binary_name):
 
 def compile(code):
     try:
-        return compile_diet(code)
+        return compile_musl(code)
     except CompilerNotFoundError:
         try:
-            return compile_musl(code)
+            return compile_diet(code)
         except CompilerNotFoundError:
             raise CompilerNotFoundError('No suiteable C compiler was found.')
 

From c15d16337cd2d7c2e8936350893edd59d64c43a1 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:12:06 -0500
Subject: [PATCH 071/101] Fix: the binary name wasn't included in the
 executable path.

---
 src/exodus_bundler/launchers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 70a8642..7aeaefa 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -34,7 +34,7 @@ def find_executable(binary_name):
         # The bundle directory.
         if re.match('[A-Fa-f0-9]{64}', basename):
             for bin_directory in ['/bin/', '/usr/bin/']:
-                candidate_executable = os.path.join(directory, basename, bin_directory)
+                candidate_executable = os.path.join(directory, basename, bin_directory, binary_name)
                 if os.path.exists(candidate_executable):
                     return candidate_executable
 

From b504d3f7f913b1cf6267c863fd9d689fd81578fd Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:20:09 -0500
Subject: [PATCH 072/101] Fix: needed to use a relative directory for the bin
 directory.

---
 src/exodus_bundler/launchers.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/exodus_bundler/launchers.py b/src/exodus_bundler/launchers.py
index 7aeaefa..ade383a 100644
--- a/src/exodus_bundler/launchers.py
+++ b/src/exodus_bundler/launchers.py
@@ -34,7 +34,9 @@ def find_executable(binary_name):
         # The bundle directory.
         if re.match('[A-Fa-f0-9]{64}', basename):
             for bin_directory in ['/bin/', '/usr/bin/']:
-                candidate_executable = os.path.join(directory, basename, bin_directory, binary_name)
+                relative_bin_directory = os.path.relpath(bin_directory, '/')
+                candidate_executable = os.path.join(directory, basename,
+                                                    relative_bin_directory, binary_name)
                 if os.path.exists(candidate_executable):
                     return candidate_executable
 

From fb223d7d4783ce161cfbc744d2cbb5fa227faf04 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:25:56 -0500
Subject: [PATCH 073/101] Add one missing escaped `$` in the `musl-gcc` script.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5b18b5c..a453134 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -48,7 +48,7 @@ jobs:
             (cat <<EOF > musl-gcc
             #!/bin/sh
 
-            current_directory="$(dirname "$(readlink -f "$0")")"
+            current_directory="\$(dirname "$(readlink -f "$0")")"
 
             exec \${current_directory}/../usr/bin/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             EOF

From 9926babe085d8905656ae37a367527388169f3e6 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:29:52 -0500
Subject: [PATCH 074/101] Specify the correct path for `gcc`.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a453134..6d34363 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -48,9 +48,9 @@ jobs:
             (cat <<EOF > musl-gcc
             #!/bin/sh
 
-            current_directory="\$(dirname "$(readlink -f "$0")")"
+            current_directory="$(dirname "$(readlink -f "$0")")"
 
-            exec \${current_directory}/../usr/bin/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
+            exec \${current_directory}/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             EOF
             )
             (cat <<EOF > ./exodus.c

From 0b62da80b12a0c32a958eb3069155c76880120a5 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:34:48 -0500
Subject: [PATCH 075/101] Add some `$` escapes.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6d34363..080261d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -48,7 +48,7 @@ jobs:
             (cat <<EOF > musl-gcc
             #!/bin/sh
 
-            current_directory="$(dirname "$(readlink -f "$0")")"
+            current_directory="\$(dirname "\$(readlink -f "\$0")")"
 
             exec \${current_directory}/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             EOF

From d495fdb5460f513292f0e5014bb6b9a490073124 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:42:01 -0500
Subject: [PATCH 076/101] Add the `x86_64-linux-musl` directory as an explicit
 depdency.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 080261d..5c25f87 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,7 +107,7 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
             strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov

From d558c7f666586314f3a8a53f05b146a74aab4e02 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:52:12 -0500
Subject: [PATCH 077/101] Switch from `gcc` to `pwd` because `gcc` is
 statically linked.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5c25f87..51d6fd5 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,8 +107,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /usr/local/bin/exodus -q gcc -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 5ce31c9be319199f38f46dde45f0692ac48f83d0 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 22:59:13 -0500
Subject: [PATCH 078/101] Include forked process system calls when running
 `strace`.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 51d6fd5..a5d0f95 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,8 +107,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From c6b9904b511c4a1e9132e1ab64989ded63b82430 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:11:17 -0500
Subject: [PATCH 079/101] Strip PID prefixes from `strace` output when using
 `-f`.

---
 src/exodus_bundler/input_parsing.py | 14 ++++++++++++++
 tests/test_input_parsing.py         |  9 +++++++++
 2 files changed, 23 insertions(+)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 45d5f43..c5d2d99 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -1,3 +1,6 @@
+import re
+
+
 # We don't actually want to include anything in these directories in bundles.
 blacklisted_directories = [
     '/dev/',
@@ -22,6 +25,7 @@
 
 def extract_exec_path(line):
     """Parse a line of strace output and returns the file being executed."""
+    line = strip_pid_prefix(line)
     for method in exec_methods:
         prefix = method + '("'
         if line.startswith(prefix):
@@ -34,6 +38,7 @@ def extract_exec_path(line):
 
 def extract_open_path(line):
     """Parse a line of strace output and returns the file being opened."""
+    line = strip_pid_prefix(line)
     for prefix in ['openat(AT_FDCWD, "', 'open("']:
         if line.startswith(prefix):
             parts = line[len(prefix):].split('", ')
@@ -51,6 +56,7 @@ def extract_open_path(line):
 
 def extract_stat_path(line):
     """Parse a line of strace output and return the file that stat was called on."""
+    line = strip_pid_prefix(line)
     prefix = 'stat("'
     if line.startswith(prefix):
         parts = line[len(prefix):].split('", ')
@@ -87,3 +93,11 @@ def extract_paths(content):
                 paths.append(path)
 
     return paths
+
+
+def strip_pid_prefix(line):
+    """Strips out the `[pid XXX] ` prefix if present."""
+    match = re.match('\[pid\s+\d+\]\s*', line)
+    if match:
+        return line[len(match.group()):]
+    return line
diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index e6101ab..f19c774 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -4,6 +4,7 @@
 from exodus_bundler.input_parsing import extract_open_path
 from exodus_bundler.input_parsing import extract_paths
 from exodus_bundler.input_parsing import extract_stat_path
+from exodus_bundler.input_parsing import strip_pid_prefix
 
 
 parent_directory = os.path.dirname(os.path.realpath(__file__))
@@ -86,3 +87,11 @@ def test_extract_strace_paths():
     for path in expected_paths:
         assert path in extracted_paths, \
             '"%s" should be present in the extracted paths.' % path
+
+def test_strip_pid_prefix():
+    line = (
+        '[pid   655] execve("/usr/bin/musl-gcc", ["/usr/bin/musl-gcc", "-static", "-O3", '
+        '"/tmp/exodus-bundle-fqzw_lds.c", "-o", "/tmp/exodus-bundle-3p_c0osh"], [/* 45 vars */] '
+        '<unfinished ...>'
+    )
+    assert strip_pid_prefix(line).startswith('execve('), 'The PID prefix should be stripped.'

From f9bfc3abbb0cff4655827257e8aa978c2f596f1c Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:24:09 -0500
Subject: [PATCH 080/101] Make the exodus bundles as root.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a5d0f95..fdf713f 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -107,8 +107,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From b5c51dabc88c6d028f2b1d9d7ad82553e6ae4cbc Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:27:22 -0500
Subject: [PATCH 081/101] Temporarily disable `extract_stat_path()`.

---
 src/exodus_bundler/input_parsing.py | 1 +
 tests/test_input_parsing.py         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index c5d2d99..a51c802 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -56,6 +56,7 @@ def extract_open_path(line):
 
 def extract_stat_path(line):
     """Parse a line of strace output and return the file that stat was called on."""
+    return None
     line = strip_pid_prefix(line)
     prefix = 'stat("'
     if line.startswith(prefix):
diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index f19c774..9e8f9fb 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -56,6 +56,7 @@ def test_extract_raw_paths():
 
 
 def test_extract_stat_path():
+    return True
     line = (
         'stat("/usr/local/lib/python3.6/encodings/__init__.py", '
         '{st_mode=S_IFREG|0644, st_size=5642, ...}) = 0'

From 7f287d125882d8c46c0582cb5edb5e030f0ebda9 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:34:29 -0500
Subject: [PATCH 082/101] Only consider existent paths from strace outputs.

---
 src/exodus_bundler/input_parsing.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index a51c802..ddb8a29 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -1,3 +1,4 @@
+import os
 import re
 
 
@@ -85,15 +86,16 @@ def extract_paths(content):
         return lines
 
     # Extract files from `open()`, `openat()`, and `exec()` calls.
-    paths = []
+    paths = set()
     for line in lines:
         path = extract_exec_path(line) or extract_open_path(line) or extract_stat_path(line)
         if path:
             blacklisted = any(path.startswith(directory) for directory in blacklisted_directories)
             if not blacklisted:
-                paths.append(path)
+                if os.path.exists(path):
+                    paths.add(path)
 
-    return paths
+    return list(paths)
 
 
 def strip_pid_prefix(line):

From ce0b602c9a0a1e30dd69b76b6501bc872c33ea37 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:47:02 -0500
Subject: [PATCH 083/101] Turn the `stat()` extraction back on.

---
 src/exodus_bundler/input_parsing.py | 1 -
 tests/test_input_parsing.py         | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index ddb8a29..4110c53 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -57,7 +57,6 @@ def extract_open_path(line):
 
 def extract_stat_path(line):
     """Parse a line of strace output and return the file that stat was called on."""
-    return None
     line = strip_pid_prefix(line)
     prefix = 'stat("'
     if line.startswith(prefix):
diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index 9e8f9fb..f19c774 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -56,7 +56,6 @@ def test_extract_raw_paths():
 
 
 def test_extract_stat_path():
-    return True
     line = (
         'stat("/usr/local/lib/python3.6/encodings/__init__.py", '
         '{st_mode=S_IFREG|0644, st_size=5642, ...}) = 0'

From fdbda4c880cd6baafdd2851895559d58f7905d6d Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:47:20 -0500
Subject: [PATCH 084/101] Require read access on files parsed from `strace`
 outputs.

---
 src/exodus_bundler/input_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 4110c53..0745c7d 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -91,7 +91,7 @@ def extract_paths(content):
         if path:
             blacklisted = any(path.startswith(directory) for directory in blacklisted_directories)
             if not blacklisted:
-                if os.path.exists(path):
+                if os.path.exists(path) and os.access(path, os.R_OK):
                     paths.add(path)
 
     return list(paths)

From c1c8162defd40d4f02346c4a4ecda9ba216670f7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:49:19 -0500
Subject: [PATCH 085/101] Disable the `stat()` calls.

---
 src/exodus_bundler/input_parsing.py | 1 +
 tests/test_input_parsing.py         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 0745c7d..476ce36 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -57,6 +57,7 @@ def extract_open_path(line):
 
 def extract_stat_path(line):
     """Parse a line of strace output and return the file that stat was called on."""
+    return None
     line = strip_pid_prefix(line)
     prefix = 'stat("'
     if line.startswith(prefix):
diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index f19c774..e9a4ccc 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -56,6 +56,7 @@ def test_extract_raw_paths():
 
 
 def test_extract_stat_path():
+    return None
     line = (
         'stat("/usr/local/lib/python3.6/encodings/__init__.py", '
         '{st_mode=S_IFREG|0644, st_size=5642, ...}) = 0'

From dff7717104553419bfe8a381c360698eb43a2654 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Sun, 4 Mar 2018 23:53:31 -0500
Subject: [PATCH 086/101] Re-enable `stat()` paths again.

---
 src/exodus_bundler/input_parsing.py | 1 -
 tests/test_input_parsing.py         | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 476ce36..0745c7d 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -57,7 +57,6 @@ def extract_open_path(line):
 
 def extract_stat_path(line):
     """Parse a line of strace output and return the file that stat was called on."""
-    return None
     line = strip_pid_prefix(line)
     prefix = 'stat("'
     if line.startswith(prefix):
diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index e9a4ccc..f19c774 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -56,7 +56,6 @@ def test_extract_raw_paths():
 
 
 def test_extract_stat_path():
-    return None
     line = (
         'stat("/usr/local/lib/python3.6/encodings/__init__.py", '
         '{st_mode=S_IFREG|0644, st_size=5642, ...}) = 0'

From 97f180cbcbda324ecd49bffb054016a2725d7be7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 08:45:59 -0500
Subject: [PATCH 087/101] Exclude directories from parsed `strace()` output.

---
 src/exodus_bundler/input_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/input_parsing.py b/src/exodus_bundler/input_parsing.py
index 0745c7d..92550e6 100644
--- a/src/exodus_bundler/input_parsing.py
+++ b/src/exodus_bundler/input_parsing.py
@@ -91,7 +91,7 @@ def extract_paths(content):
         if path:
             blacklisted = any(path.startswith(directory) for directory in blacklisted_directories)
             if not blacklisted:
-                if os.path.exists(path) and os.access(path, os.R_OK):
+                if os.path.exists(path) and os.access(path, os.R_OK) and not os.path.isdir(path):
                     paths.add(path)
 
     return list(paths)

From 45c988fad8bb36d12f9513ad8aac69b3139722d3 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:17:16 -0500
Subject: [PATCH 088/101] Switch to using python 2.

---
 .circleci/config.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index fdf713f..4f5c9c2 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -44,7 +44,8 @@ jobs:
       - run:
           name: Build Self-Hosted Bundle
           command: |
-            sudo pip install .
+            sudo apt-get install python-pip
+            sudo pip2 install .
             (cat <<EOF > musl-gcc
             #!/bin/sh
 
@@ -67,7 +68,7 @@ jobs:
 
                     char python[4096] = { 0 };
                     strcpy(python, current_directory);
-                    strcat(python, "/usr/local/bin/python");
+                    strcat(python, "/usr/bin/python");
 
                     char exodus[4096] = { 0 };
                     strcpy(exodus, current_directory);
@@ -89,7 +90,7 @@ jobs:
                     char pythonpath[4096] = { 0 };
                     strcpy(pythonpath, "PYTHONPATH=");
                     strcat(pythonpath, current_directory);
-                    strcat(pythonpath, "/usr/local/lib/python3.6/");
+                    strcat(pythonpath, "/usr/local/lib/python2.7/");
                     envp[1] = pythonpath;
 
                     envp[2] = NULL;
@@ -107,8 +108,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f python /usr/local/bin/exodus -q pwd -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python3.6/site-packages/exodus_bundler/ --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python3.6/site-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python "print 'hello world'" -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python "print 'hello world'" -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 0bb3287138dab650ef6550a903714961560ec49c Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:20:22 -0500
Subject: [PATCH 089/101] No longer set PYTHONHOME.

---
 .circleci/config.yml | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4f5c9c2..63dc0c7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -80,20 +80,14 @@ jobs:
                     memcpy(combined_args + 2, argv + 1, sizeof(char*) * (argc - 1));
                     combined_args[argc + 1] = NULL;
 
-                    char *envp[3];
-                    char pythonhome[4096] = { 0 };
-                    strcpy(pythonhome, "PYTHONHOME=");
-                    strcat(pythonhome, current_directory);
-                    strcat(pythonhome, "/usr/local/");
-                    envp[0] = pythonhome;
-
+                    char *envp[2];
                     char pythonpath[4096] = { 0 };
                     strcpy(pythonpath, "PYTHONPATH=");
                     strcat(pythonpath, current_directory);
                     strcat(pythonpath, "/usr/local/lib/python2.7/");
-                    envp[1] = pythonpath;
+                    envp[0] = pythonpath;
 
-                    envp[2] = NULL;
+                    envp[1] = NULL;
 
                     execve(python, combined_args, envp);
                 }

From 05513f75889fae6912572c4a4e1fa2b73fc35cc2 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:24:02 -0500
Subject: [PATCH 090/101] Fix the first exodus invocations.

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 63dc0c7..cf8359a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -102,8 +102,8 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python "print 'hello world'" -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python "print 'hello world'" -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From 5cd7f372605d5c2456f6d01518c76b247eadad12 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:28:21 -0500
Subject: [PATCH 091/101] Try bundling without the ld cache.

---
 .circleci/config.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index cf8359a..75d174e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -102,8 +102,10 @@ jobs:
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
+            sudo mv /etc/ld.so.cache /tmp/ld.so.cache.bck
             strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
             strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            sudo mv /tmp/ld.so.cache.bck /etc/ld.so.cache
       - store_artifacts:
           path: htmlcov
           destination: coverage-report

From ca2b90b51c9e9a905c1c553a0f32f7c81637dfab Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:37:53 -0500
Subject: [PATCH 092/101] Bundle as an unprivileged user.

---
 .circleci/config.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 75d174e..8e06a9b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -101,10 +101,11 @@ jobs:
             sudo chmod a+x /usr/bin/musl-gcc
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
-            export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
+            sudo chmod a+x /exodus
             sudo mv /etc/ld.so.cache /tmp/ld.so.cache.bck
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | sudo exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
             sudo mv /tmp/ld.so.cache.bck /etc/ld.so.cache
       - store_artifacts:
           path: htmlcov

From dc78e3434ead0adbd1079094ee8e1dfeb11aef19 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 09:54:40 -0500
Subject: [PATCH 093/101] Try it with clang instead of gcc.

---
 .circleci/config.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 8e06a9b..feb1447 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,15 +45,17 @@ jobs:
           name: Build Self-Hosted Bundle
           command: |
             sudo apt-get install python-pip
+            sudo apt-get install clang
             sudo pip2 install .
             (cat <<EOF > musl-gcc
             #!/bin/sh
 
             current_directory="\$(dirname "\$(readlink -f "\$0")")"
 
-            exec \${current_directory}/gcc "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
+            exec \${current_directory}/clang "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
             EOF
             )
+
             (cat <<EOF > ./exodus.c
             #include <libgen.h>
             #include <stdlib.h>

From 44ad57f58c6d295df658e9c669dcdfa7c8522981 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 10:03:24 -0500
Subject: [PATCH 094/101] Add `/usr/lib/x86_64-linux-gnu/` to LD_LIBRARY_PATH.

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index feb1447..e4ab884 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -105,7 +105,7 @@ jobs:
             sudo musl-gcc -static -O3 exodus.c -o exodus
             sudo chmod a+x /exodus
             sudo mv /etc/ld.so.cache /tmp/ld.so.cache.bck
-            export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
+            export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:/usr/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
             strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
             strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
             sudo mv /tmp/ld.so.cache.bck /etc/ld.so.cache

From f295f13cf8e5c8592c7668cc29c86aea08b64ec7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 10:43:28 -0500
Subject: [PATCH 095/101] Cut losses and make a bundle without the compilers.

---
 .circleci/config.yml | 24 +++++++++---------------
 1 file changed, 9 insertions(+), 15 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e4ab884..6c3431a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -22,7 +22,6 @@ jobs:
             python3 -m venv .env
             . .env/bin/activate
             pip install -r development-requirements.txt
-            sudo apt-get install gcc musl musl-tools patchelf python-dev strace
       - save_cache:
           paths:
             - ./.env
@@ -44,17 +43,8 @@ jobs:
       - run:
           name: Build Self-Hosted Bundle
           command: |
-            sudo apt-get install python-pip
-            sudo apt-get install clang
+            sudo apt-get install gcc musl musl-tools python-pip strace
             sudo pip2 install .
-            (cat <<EOF > musl-gcc
-            #!/bin/sh
-
-            current_directory="\$(dirname "\$(readlink -f "\$0")")"
-
-            exec \${current_directory}/clang "\$@" -nostdinc -nostdlib -I\${current_directory}/../../usr/include/x86_64-linux-musl -L\${current_directory}/../../usr/lib/x86_64-linux-musl \${current_directory}/../../usr/lib/x86_64-linux-musl/crt1.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crti.o \${current_directory}/../../usr/lib/x86_64-linux-musl/crtn.o -lc
-            EOF
-            )
 
             (cat <<EOF > ./exodus.c
             #include <libgen.h>
@@ -99,15 +89,19 @@ jobs:
             EOF
             )
             sudo cp exodus.c /
-            sudo cp musl-gcc /usr/bin/musl-gcc
-            sudo chmod a+x /usr/bin/musl-gcc
             cd /
             sudo musl-gcc -static -O3 exodus.c -o exodus
             sudo chmod a+x /exodus
+
+            # The compiler won't bundle correctly, so we can at least temporarily move this and then be able to create bash launchers.
+            sudo mv /usr/bin/musl-gcc /tmp/musl-gcc.bck
             sudo mv /etc/ld.so.cache /tmp/ld.so.cache.bck
+
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:/usr/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --add /usr/lib/x86_64-linux-musl/ --no-symlink /usr/bin/musl-gcc --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --no-symlink /usr/bin/musl-gcc --output /home/circleci/exodus/exodus-x64.sh
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --output /home/circleci/exodus/exodus-x64.sh
+
+            sudo mv /tmp/musl-gcc.bck /usr/bin/musl-gcc
             sudo mv /tmp/ld.so.cache.bck /etc/ld.so.cache
       - store_artifacts:
           path: htmlcov

From d122766da04a51626326644c26a43299169f18a7 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:08:02 -0500
Subject: [PATCH 096/101] Add a `--shell-launchers` flag for forcing the use of
 shell launchers.

---
 src/exodus_bundler/bundling.py | 26 +++++++++++++++++++-------
 src/exodus_bundler/cli.py      |  4 ++++
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 02aa808..eac85e4 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -38,7 +38,7 @@ def bytes_to_int(bytes, byteorder='big'):
 
 
 def create_bundle(executables, output, tarball=False, rename=[], chroot=None, add=[],
-                  no_symlink=[]):
+                  no_symlink=[], shell_launchers=False):
     """Handles the creation of the full bundle."""
     # Initialize these ahead of time so they're always available for error handling.
     output_filename, output_file, root_directory = None, None, None
@@ -46,7 +46,9 @@ def create_bundle(executables, output, tarball=False, rename=[], chroot=None, ad
 
         # Create a temporary unpackaged bundle for the executables.
         root_directory = create_unpackaged_bundle(
-            executables, rename=rename, chroot=chroot, add=add, no_symlink=no_symlink)
+            executables, rename=rename, chroot=chroot, add=add, no_symlink=no_symlink,
+            shell_launchers=shell_launchers,
+        )
 
         # Populate the filename template.
         output_filename = render_template(output,
@@ -94,7 +96,8 @@ def create_bundle(executables, output, tarball=False, rename=[], chroot=None, ad
                 os.chmod(output_filename, st.st_mode | stat.S_IEXEC)
 
 
-def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[], no_symlink=[]):
+def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[], no_symlink=[],
+                             shell_launchers=False):
     """Creates a temporary directory containing the unpackaged contents of the bundle."""
     bundle = Bundle(chroot=chroot, working_directory=True)
     try:
@@ -476,7 +479,8 @@ def create_entry_point(self, working_directory, bundle_root):
         relative_destination_path = os.path.relpath(source_path, bin_directory)
         os.symlink(relative_destination_path, entry_point_path)
 
-    def create_launcher(self, working_directory, bundle_root, linker_basename, symlink_basename):
+    def create_launcher(self, working_directory, bundle_root, linker_basename, symlink_basename,
+                        shell_launcher=False):
         """Creates a launcher at `source` for `destination`.
 
         Note:
@@ -486,6 +490,8 @@ def create_launcher(self, working_directory, bundle_root, linker_basename, symli
             bundle_root (str): The root that `source` will be joined with.
             linker_basename (str): The basename of the linker to place in the same directory.
             symlink_basename (str): The basename of the symlink to the actual executable.
+            shell_launcher (bool, optional): Forces the use of shell script launcher instead of
+                attempting to compile first using musl or diet c.
         Returns:
             str: The normalized and absolute path to the launcher.
         """
@@ -677,8 +683,13 @@ def add_file(self, path, entry_point=None):
         if file.elf:
             self.files |= file.elf.dependencies
 
-    def create_bundle(self):
-        """Creates the unpackaged bundle in `working_directory`."""
+    def create_bundle(self, shell_launchers=False):
+        """Creates the unpackaged bundle in `working_directory`.
+
+        Args:
+            shell_launchers (bool, optional): Forces the use of shell script launchers instead of
+                attempting to compile first using musl or diet c.
+        """
         file_paths = set()
         files_needing_launchers = defaultdict(set)
         for file in self.files:
@@ -740,7 +751,8 @@ def create_bundle(self):
                 file_paths.add(symlink_path)
                 symlink_basename = os.path.basename(symlink_path)
                 file.create_launcher(self.working_directory, self.bundle_root,
-                                     linker_basename, symlink_basename)
+                                     linker_basename, symlink_basename,
+                                     shell_launcher=shell_launchers)
 
     def delete_working_directory(self):
         """Recursively deletes the working directory."""
diff --git a/src/exodus_bundler/cli.py b/src/exodus_bundler/cli.py
index ee79adf..61d1f0a 100644
--- a/src/exodus_bundler/cli.py
+++ b/src/exodus_bundler/cli.py
@@ -74,6 +74,10 @@ def parse_args(args=None, namespace=None):
         ),
     )
 
+    parser.add_argument('--shell-launchers', action='store_true', help=(
+        'Force the use of shell launchers instead of attempting to compile statically linked ones.'
+    ))
+
     parser.add_argument('-t', '--tarball', action='store_true', help=(
         'Creates a tarball for manual extraction instead of an installation script. '
         'Note that this will change the output extension from ".sh" to ".tgz".'

From cfd5499ed30e30f04a5a653110e169289c4d937b Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:08:23 -0500
Subject: [PATCH 097/101] Use the `--shell-launchers` flag during
 self-bundling.

---
 .circleci/config.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6c3431a..eee47c7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -93,15 +93,12 @@ jobs:
             sudo musl-gcc -static -O3 exodus.c -o exodus
             sudo chmod a+x /exodus
 
-            # The compiler won't bundle correctly, so we can at least temporarily move this and then be able to create bash launchers.
-            sudo mv /usr/bin/musl-gcc /tmp/musl-gcc.bck
             sudo mv /etc/ld.so.cache /tmp/ld.so.cache.bck
 
             export LD_LIBRARY_PATH=/usr/local/lib/:/lib/x86_64-linux-gnu/:/usr/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --tar --output /home/circleci/exodus/exodus-x64.tgz
-            strace -f /usr/bin/python /usr/local/bin/exodus -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --output /home/circleci/exodus/exodus-x64.sh
+            strace -f /usr/bin/python /usr/local/bin/exodus --shell-launchers -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --tar --output /home/circleci/exodus/exodus-x64.tgz
+            strace -f /usr/bin/python /usr/local/bin/exodus --shell-launchers -q /usr/bin/python -o /dev/null 2>&1 | exodus ./exodus --add /usr/local/lib/python2.7/dist-packages/exodus_bundler/ --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/templating.py --no-symlink /usr/local/lib/python2.7/dist-packages/exodus_bundler/launchers.py --output /home/circleci/exodus/exodus-x64.sh
 
-            sudo mv /tmp/musl-gcc.bck /usr/bin/musl-gcc
             sudo mv /tmp/ld.so.cache.bck /etc/ld.so.cache
       - store_artifacts:
           path: htmlcov

From f3678da1dda0e2dd5c34f6f31805ec709df4e6cf Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:08:39 -0500
Subject: [PATCH 098/101] Fix linting whitespace issue.

---
 tests/test_input_parsing.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_input_parsing.py b/tests/test_input_parsing.py
index f19c774..1903d02 100644
--- a/tests/test_input_parsing.py
+++ b/tests/test_input_parsing.py
@@ -88,6 +88,7 @@ def test_extract_strace_paths():
         assert path in extracted_paths, \
             '"%s" should be present in the extracted paths.' % path
 
+
 def test_strip_pid_prefix():
     line = (
         '[pid   655] execve("/usr/bin/musl-gcc", ["/usr/bin/musl-gcc", "-static", "-O3", '

From 8ac0c2d065af3729ba7fdd6bbc4ee798ee593ce0 Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:10:30 -0500
Subject: [PATCH 099/101] Raise a `CompilerNotFoundError` when
 `--shell-launchers` is specified.

---
 src/exodus_bundler/bundling.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index eac85e4..61ecfb6 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -537,6 +537,9 @@ def create_launcher(self, working_directory, bundle_root, linker_basename, symli
 
         # Try a c launcher first and fallback.
         try:
+            if shell_launcher:
+                raise CompilerNotFoundError()
+
             launcher_content = construct_binary_launcher(
                 linker=linker, library_path=library_path, executable=executable)
             with open(source_path, 'wb') as f:

From b2fc939d28774d63301d8416de331e0a7ae44efb Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:15:23 -0500
Subject: [PATCH 100/101] Fix: wasn't passing `shell_launchers` along as an
 argument.

---
 src/exodus_bundler/bundling.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 61ecfb6..50c2ba0 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -123,7 +123,7 @@ def create_unpackaged_bundle(executables, rename=[], chroot=None, add=[], no_sym
             if file:
                 file.no_symlink = True
 
-        bundle.create_bundle()
+        bundle.create_bundle(shell_launchers=shell_launchers)
 
         return bundle.working_directory
     except:  # noqa: E722

From 38a511bbd1843b21c35d41e7e076d84a4435f58e Mon Sep 17 00:00:00 2001
From: Evan Sangaline <esangaline@gmail.com>
Date: Mon, 5 Mar 2018 11:15:57 -0500
Subject: [PATCH 101/101] Don't display the fallback warning when
 `--shell-launchers` is specified.

---
 src/exodus_bundler/bundling.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/exodus_bundler/bundling.py b/src/exodus_bundler/bundling.py
index 50c2ba0..aa7ef34 100644
--- a/src/exodus_bundler/bundling.py
+++ b/src/exodus_bundler/bundling.py
@@ -545,10 +545,11 @@ def create_launcher(self, working_directory, bundle_root, linker_basename, symli
             with open(source_path, 'wb') as f:
                 f.write(launcher_content)
         except CompilerNotFoundError:
-            logger.warn((
-                'Installing either the musl or diet C libraries will result in more efficient '
-                'launchers (currently using bash fallbacks instead).'
-            ))
+            if not shell_launcher:
+                logger.warn((
+                    'Installing either the musl or diet C libraries will result in more efficient '
+                    'launchers (currently using bash fallbacks instead).'
+                ))
             launcher_content = construct_bash_launcher(
                 linker=linker, library_path=library_path, executable=executable)
             with open(source_path, 'w') as f: