updating for pip 19

.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:

.circleci/requirements.txt

@@ -0,0 +1,5 @@
+# third party forks
+git+https://github.com/KarrLab/log.git#egg=log
+
+# Karr Lab
+git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils

Dockerfile

@@ -3,8 +3,8 @@ FROM karrlab/wc_env_dependencies
 # install and configure software and examples
 RUN git clone https://github.com/KarrLab/wc_sandbox.git \
     && cd /root/wc_sandbox \
-    && pip3.6 install --process-dependency-links -r requirements.txt \
-    && pip3.6 install --process-dependency-links -e . \
+    && pip3.6 install -r ./circleci/requirements.txt \
+    && pip3.6 install -e . \
     \
     && jupyter contrib nbextension install \
     && jupyter nbextensions_configurator disable \

README.md

@@ -27,7 +27,9 @@ WC-Sandbox is a collection of Jupyter notebooks for learning about whole-cell mo
 
     * Install the latest revision from GitHub
       ```
-      pip install git+git://github.com/KarrLab/wc_sandbox#egg=wc_sandbox
+      pip install git+https://github.com/KarrLab/log.git#egg=log
+      pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
+      pip install git+https://github.com/KarrLab/wc_sandbox.git#egg=wc_sandbox
       ```
 
 ## Examples, tutorial, and documentation

docs/installation.rst

@@ -18,4 +18,6 @@ Latest revision from GitHub
 ---------------------------
 Run the following command to install the latest version from GitHub::
 
-    pip install git+git://github.com/KarrLab/wc_sandbox.git#egg=wc_sandbox
+    pip install git+https://github.com/KarrLab/log.git#egg=log
+    pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
+    pip install git+https://github.com/KarrLab/wc_sandbox.git#egg=wc_sandbox

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

requirements.txt

@@ -11,4 +11,4 @@ configobj # configuration
 cement # CLI
 gitpython
 setuptools # pkg_resources
-git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils-0.0.3 >= 0.0.3
+wc_utils >= 0.0.3

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
 

wc_sandbox/__main__.py

@@ -68,7 +68,11 @@ def _default(self):
                 git.Repo.clone_from('https://github.com/KarrLab/{}.git'.format(package_id), package_path)
 
             py_v = '{}.{}'.format(sys.version_info[0], sys.version_info[1])
-            cmd = ['pip' + py_v, 'install', '--process-dependency-links', '-e', package_path]
+
+            cmd = ['pip' + py_v, 'install', '-r', os.path.join(package_path, '.circleci', 'requirements.txt')]
+            subprocess.check_call(cmd)
+
+            cmd = ['pip' + py_v, 'install', '-e', package_path]
             subprocess.check_call(cmd)
 
         print('Installed packages:\n- {}'.format('\n- '.join(sorted(package_ids))))