Merge branch '1.0.x' into 'master'

.github/workflows/test.yml

@@ -76,7 +76,6 @@ jobs:
                 ;;
             checks)
                 flake8 --ignore=E731,W504
-                find scripts -name '*.py' -exec flake8 {} +
                 diff -q reprozip/reprozip/common.py reprounzip/reprounzip/common.py
                 diff -q reprozip/reprozip/utils.py reprounzip/reprounzip/utils.py
                 find reprozip reprounzip reprozip-* reprounzip-* .travis -name '*.py' -or -name '*.sh' -or -name '*.h' -or -name '*.c' | (set +x; while read i; do

docs/install.rst

@@ -175,7 +175,7 @@ Besides Python and pip, each component or plugin to be used may have additional
 ..  [#bug3] ``reprozip`` and ``reprounzip graph`` will not work before 2.7.3 due to `Python bug 13676 <https://bugs.python.org/issue13676>`__ related to sqlite3. Python 2.6 is ancient and unsupported.
 ..  [#pycrypto3] A working C compiler is required to build PyCrypto. For installation without building from source, please see `this page <https://stackoverflow.com/questions/11405549/how-do-i-install-pycrypto-on-windows>`__.
 ..  [#vis3] `VisTrails v2.2.3+ <https://www.vistrails.org/>`__ is required to run the workflow generated by the plugin.
-..  [#windowshome] Windows Professional Edition is required for Docker, it will not work on Windows Home Edition; `see FAQ <https://docs.docker.com/docker-for-windows/faqs/#why-is-windows-10-home-not-supported#can-i-install-docker-desktop-on-windows-10-home>`__.
+..  [#windowshome] Windows Professional Edition is required for Docker, it will not work on Windows Home Edition; `see FAQ <https://docs.docker.com/docker-for-windows/faqs/#can-i-install-docker-desktop-on-windows-10-home>`__.
 
 Installing *reprounzip*
 -----------------------

docs/packing.rst

@@ -181,18 +181,27 @@ When reproducing an experiment that communicates with a server, the experiment w
 
 and use *reprozip* to trace the script execution, rather than the experiment itself. In this way, ReproZip is able to capture the local server as well, which ensures that the server will be alive at the time of the reproduction.
 
-For example, if you have an web app that uses PostgreSQL and that runs until ``Ctrl+C`` is received, you can use the following script::
+For example, if you have an web app that uses MySQL and that runs until ``Ctrl+C`` is received, you can use the following script::
 
     #!/bin/sh
 
-    /etc/init.d/postgresql start        # Start PostgreSQL
+    if [ "$(id -u)" != 0 ]; then echo "This script needs to run as root so that it can execute MySQL" >&2; exit 1; fi
 
-    trap ' ' INT                        # Don't exit the whole script on Ctrl+C
+    # Start MySQL
+    sudo -u mysql /usr/sbin/mysqld --pid-file=/run/mysqld/mysqld.pid &
+    sleep 5
+
+    # Don't exit the whole script on Ctrl+C
+    trap ' ' INT
+
+    # Execute actual experiment that uses the database
     ./manage.py runserver 0.0.0.0:8000
+
     trap - INT
 
-    /etc/init.d/postgresql stop         # Stop PostgreSQL
-    
+    # Graceful shutdown
+    /usr/bin/mysqladmin shutdown
+
 Note the use of ``trap`` to avoid exiting the entire script when pressing ``Ctrl+C``, to make sure that the database gets shutdown via the next command.
 
 Excluding Sensitive and Third-Party Information

docs/troubleshooting.rst

@@ -25,16 +25,12 @@ Please feel free to contact us at users@reprozip.org if you encounter issues whi
 
                $ reprozip trace service mysql start
 
-           you can trace either the `init` script::
-
-               $ reprozip trace /etc/init.d/mysql start
-
-           or the binary::
+           you can trace the binary::
 
                $ reprozip trace /usr/bin/mysqld
 
            Note that, if you choose to trace the binary, you need to figure out the right command line options to use.
-           Also, make sure that systemd is not called, since ReproZip and systemd currently do not get along well.
+           Also, note that running the init script in ``/etc/init.d/...`` is not enough, since those scripts get subverted to call `systemctl` when systemd is installed.
 
 ------------
 

reprounzip/reprounzip/unpackers/common/packages.py

@@ -69,8 +69,8 @@ def get_packages_info(packages):
         pkgs_dict = dict((pkg.name, (pkg, PKG_NOT_INSTALLED))
                          for pkg in packages)
         try:
-            for l in p.stdout:
-                fields = l.split()
+            for line in p.stdout:
+                fields = line.split()
                 if len(fields) == 2:
                     name = fields[0].decode('ascii')
                     status = fields[1].decode('ascii')
@@ -124,9 +124,9 @@ def get_packages_info(packages):
         pkgs_dict = dict((pkg.name, (pkg, PKG_NOT_INSTALLED))
                          for pkg in packages)
         try:
-            for l in p.stdout:
-                if l[0] == b'+':
-                    fields = l[1:].split()
+            for line in p.stdout:
+                if line[0] == b'+':
+                    fields = line[1:].split()
                     if len(fields) == 2:
                         name = fields[0].decode('ascii')
                         status = fields[1].decode('ascii')

reprounzip/reprounzip/unpackers/default.py

@@ -210,11 +210,11 @@ def directory_run(args):
                          stderr=subprocess.PIPE)
     stdout, _ = p.communicate()
     try:
-        for l in stdout.splitlines():
-            if len(l) < 2 or l[0] in (b' ', b'\t'):
+        for line in stdout.splitlines():
+            if len(line) < 2 or line[0] in (b' ', b'\t'):
                 continue
-            if l.endswith(b':'):
-                lib_dirs.append(Path(l[:-1]))
+            if line.endswith(b':'):
+                lib_dirs.append(Path(line[:-1]))
     finally:
         if p.returncode != 0:
             raise subprocess.CalledProcessError(p.returncode,

reprozip/reprozip/tracer/linux_pkgs.py

@@ -132,8 +132,8 @@ def search_for_files(self, files):
                                     stdout=subprocess.PIPE,
                                     stderr=subprocess.PIPE)
             out, err = proc.communicate()
-            for l in out.splitlines():
-                pkgname, path = l.split(b': ', 1)
+            for line in out.splitlines():
+                pkgname, path = line.split(b': ', 1)
                 path = Path(path.strip())
                 # 8-bit safe encoding, because this might be a localized error
                 # message (that we don't care about)

scripts/conda/conda.py

@@ -67,8 +67,8 @@ def build_pkg(python_ver, package_name):
         with open(join(temp_dir, package_name, 'meta.yaml')) as fp:
             lines = fp.readlines()
         # Changes version in recipe
-        lines = [l.replace('_REPLACE_version_REPLACE_', version)
-                 for l in lines]
+        lines = [line.replace('_REPLACE_version_REPLACE_', version)
+                 for line in lines]
         with open(join(temp_dir, package_name, 'meta.yaml'), 'w') as fp:
             for line in lines:
                 # Changes version

tests/functional.py

@@ -173,13 +173,13 @@ def functional_tests(raise_warnings, interactive, run_vagrant, run_docker):
     #
 
     output = check_output(rpz + ['testrun', '/bin/echo', 'outputhere'])
-    assert any(b' 1 | /bin/echo outputhere ' in l
-               for l in output.splitlines())
+    assert any(b' 1 | /bin/echo outputhere ' in line
+               for line in output.splitlines())
 
     output = check_output(rpz + ['testrun', '-a', '/fake/path/echo',
                                  '/bin/echo', 'outputhere'])
-    assert any(b' 1 | (/bin/echo) /fake/path/echo outputhere ' in l
-               for l in output.splitlines())
+    assert any(b' 1 | (/bin/echo) /fake/path/echo outputhere ' in line
+               for line in output.splitlines())
 
     # ########################################
     # testrun multiple commands
@@ -549,8 +549,8 @@ def check_simple(args, stream, infile=1):
     build('threads', ['threads.c'], ['-lpthread'])
     # Trace
     output = check_output(rpz + ['testrun', './threads'], 'err')
-    assert any(b'successfully exec\'d /bin/./echo' in l
-               for l in output.splitlines())
+    assert any(b'successfully exec\'d /bin/./echo' in line
+               for line in output.splitlines())
 
     # ########################################
     # 'threads2' program: testrun
@@ -560,8 +560,8 @@ def check_simple(args, stream, infile=1):
     build('threads2', ['threads2.c'], ['-lpthread'])
     # Trace
     output = check_output(rpz + ['testrun', './threads2'], 'err')
-    assert any(b'successfully exec\'d /bin/echo' in l
-               for l in output.splitlines())
+    assert any(b'successfully exec\'d /bin/echo' in line
+               for line in output.splitlines())
 
     # ########################################
     # 'segv' program: testrun
@@ -634,9 +634,10 @@ def check_simple(args, stream, infile=1):
     # Trace
     err = check_output(rpz + ['testrun', './connect'], 'err')
     err = err.split(b'\n')
-    assert not any(b'program exited with non-zero code' in l for l in err)
-    assert any(re.search(br'process connected to [0-9.]+:80', l)
-               for l in err)
+    assert not any(b'program exited with non-zero code' in line
+                   for line in err)
+    assert any(re.search(br'process connected to [0-9.]+:80', line)
+               for line in err)
 
     # ########################################
     # 'vfork' program: testrun
@@ -647,7 +648,8 @@ def check_simple(args, stream, infile=1):
     # Trace
     err = check_output(rpz + ['testrun', './vfork'], 'err')
     err = err.split(b'\n')
-    assert not any(b'program exited with non-zero code' in l for l in err)
+    assert not any(b'program exited with non-zero code' in line
+                   for line in err)
 
     # ########################################
     # 'rename' program: trace
@@ -813,7 +815,7 @@ def check_simple(args, stream, infile=1):
                                 '94627ebfafbf81cd77a17d4ed646a80c94bf4202'],
                          'err')
     err = err.split(b'\n')
-    assert any(b'executing set-uid binary!' in l for l in err)
+    assert any(b'executing set-uid binary!' in line for line in err)
 
     # ########################################
     # Test set-gid warning
@@ -828,7 +830,7 @@ def check_simple(args, stream, infile=1):
     # Pass a wrong username to su to make it exit without reading a password
     _, err = call_output(rpz + ['testrun', executable, '-l'], 'err')
     err = err.split(b'\n')
-    assert any(b'executing set-gid binary!' in l for l in err)
+    assert any(b'executing set-gid binary!' in line for line in err)
 
     # ########################################
     # Test old packages

tests/test_reprozip.py

@@ -215,9 +215,9 @@ def fail(s):
                                   set(fi.path for fi in files))
             self.assertEqualPaths([set(["/some/r", "/some/rw"]),
                                    set(["/some/cli", "/some/r"])],
-                                  [set(l) for l in inputs])
+                                  [set(run) for run in inputs])
             self.assertEqualPaths([set(["/some/cli"]), set(["/some/rw"])],
-                                  [set(l) for l in outputs])
+                                  [set(run) for run in outputs])
         finally:
             Path.is_file, Path.stat = old