From 350a4c8dc6a8c7798e989f315340d2a39257cfe2 Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Wed, 13 Mar 2019 01:42:38 -0400
Subject: [PATCH] updating for pip 19

---
 .circleci/config.yml  | 18 +++++++++++-------
 README.md             | 12 +++++++++---
 docs/installation.rst | 13 +++++++------
 docs/requirements.txt |  2 +-
 setup.py              |  2 +-
 5 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 85c08ee..90ff81e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -16,22 +16,26 @@ jobs:
       # Python 3 installation tasks
       - run:
           name: Install pkg_utils (Python 3)
-          command: pip3 install -U --process-dependency-links git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
+          command: pip3 install -U git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
       - run:
           name: Install karr_lab_build_utils (Python 3)
-          command: pip3 install -U --process-dependency-links git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
+          command: |
+            pip3 install -U git+https://github.com/KarrLab/log.git#egg=log
+            pip3 install -U git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics
+            pip3 install -U git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]
+            pip3 install -U git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils[all]
       - run:
           name: Install package configuration files including credentials
           command: karr_lab_build_utils3 download-install-package-config-files
       - run:
-          name: Install and upgrade requirements (Python 3)
+          name: Setup Python environment
           command: |
-            set +e
-            karr_lab_build_utils3 install-requirements
-            karr_lab_build_utils3 upgrade-karr-lab-packages
+            if [[ -f .circleci/requirements.txt ]]; then
+              pip3 install -U -r .circleci/requirements.txt
+            fi
       - run:
           name: Install package (Python 3)
-          command: pip3 install -U --process-dependency-links -e .[all]
+          command: pip3 install -U -e .[all]
 
       # Save packages to cache
       - save_cache:
diff --git a/README.md b/README.md
index 27d349e..3038c78 100644
--- a/README.md
+++ b/README.md
@@ -15,9 +15,15 @@ Convert [nose](http://nose.readthedocs.io)-style XML test reports to [UnitTH](ht
 * [UnitTH HTML test history report](https://cdn.rawgit.com/KarrLab/nose2unitth/master/examples/html/index.html)
 
 ## Installation
-```
-pip install nose2unitth
-```
+* Latest release from PyPI
+  ```
+  pip install nose2unitth
+  ```
+
+* Latest revision from GitHub
+  ```
+  pip install git+https://github.com/KarrLab/nose2unitth.git#egg=nose2unitth
+  ```
 
 ## Usage
 ```
diff --git a/docs/installation.rst b/docs/installation.rst
index 257d149..8313695 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -7,14 +7,15 @@ Prerequisites
 * Python
 * Pip
 
-Latest revision from GitHub
----------------------------
-Run the following command to install the latest version from GitHub::
-
-    pip install git+git://github.com/KarrLab/nose2unitth.git#egg=nose2unitth
-
 Latest release From PyPI
 ---------------------------
 Run the following command to install the latest release from PyPI::
 
     pip install nose2unitth
+
+Latest revision from GitHub
+---------------------------
+Run the following command to install the latest version from GitHub::
+
+    pip install git+https://github.com/KarrLab/nose2unitth.git#egg=nose2unitth
+
diff --git a/docs/requirements.txt b/docs/requirements.txt
index eab0c11..b225ae6 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,6 +2,6 @@ sphinx >= 1.8
 sphinx_rtd_theme >= 0.4.2
 sphinxcontrib_addmetahtml >= 0.1.1
 sphinxcontrib_bibtex
-git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics-0.1.1 >= 0.1.1
+sphinxcontrib_googleanalytics >= 0.1.1
 sphinxcontrib_spelling
 sphinxprettysearchresults
diff --git a/setup.py b/setup.py
index c6ef877..8040c33 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
     import pkg_utils
 except ImportError:
     import pip._internal
-    pip._internal.main(['install', '--process-dependency-links', 'git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils'])
+    pip._internal.main(['install', 'pkg_utils'])
     import pkg_utils
 import os