Merge commit '11d4c70809b316dae49fe515e7bec644e30b3efa'

# Conflicts:
#	docs/source/conf.py
#	modelseedpy/biochem/modelseed_biochem.py
#	modelseedpy/biochem/modelseed_builder.py
#	modelseedpy/biochem/modelseed_compound.py
#	modelseedpy/biochem/modelseed_reaction.py
#	modelseedpy/biochem/modelseed_to_cobra.py
#	modelseedpy/biochem/seed_object.py
#	modelseedpy/community/mscommunity.py
#	modelseedpy/community/mscompatibility.py
#	modelseedpy/config.cfg
#	modelseedpy/core/__init__.py
#	modelseedpy/core/biolog.py
#	modelseedpy/core/exceptions.py
#	modelseedpy/core/fbahelper.py
#	modelseedpy/core/gapfillinghelper.py
#	modelseedpy/core/msatpcorrection.py
#	modelseedpy/core/msbuilder.py
#	modelseedpy/core/msgapfill.py
#	modelseedpy/core/msgenome.py
#	modelseedpy/core/msgenomeclassifier.py
#	modelseedpy/core/msgrowthphenotypes.py
#	modelseedpy/core/msmedia.py
#	modelseedpy/core/msmodelutl.py
#	modelseedpy/core/mstemplate.py
#	modelseedpy/core/rast_client.py
#	modelseedpy/fbapkg/basefbapkg.py
#	modelseedpy/fbapkg/bilevelpkg.py
#	modelseedpy/fbapkg/flexiblebiomasspkg.py
#	modelseedpy/fbapkg/fluxfittingpkg.py
#	modelseedpy/fbapkg/gapfillingpkg.py
#	modelseedpy/fbapkg/kbasemediapkg.py
#	modelseedpy/fbapkg/reactionusepkg.py
#	modelseedpy/helpers.py
#	modelseedpy/ml/build_classifier.py
#	modelseedpy/ml/predict_phenotype.py
#	tests/biochem/test_modelseed_biochem.py
#	tests/community/test_mscommunity.py
#	tests/context.py
#	tests/core/test_msatpcorreption.py
#	tests/core/test_msbuilder.py
#	tests/core/test_msgapfill.py
#	tests/core/test_msgenome.py
#	tests/test_data/mock_data.py
#	tests/test_data/mseditorapi_testing.py

Author: cshenry

.github/workflows/pre-commit.yml

@@ -0,0 +1,25 @@
+name: Run Pre-Commit
+
+on:
+  pull_request: {}
+  push:
+    branches:
+      - dev
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.8', '3.9', '3.10']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set file mode to false
+        run: |
+          git config core.filemode false
+      - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: fix-encoding-pragma
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: debug-statements
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-byte-order-marker
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+        types: [python]
+      - id: check-vcs-permalinks
+      - id: check-symlinks
+      - id: mixed-line-ending
+      - id: name-tests-test
+        exclude: tests/test_data
+        args:
+          - --pytest-test-first
+      - id: check-json
+      - id: pretty-format-json
+        args:
+          - --autofix
+          - --top-keys=_id
+      - id: check-yaml
+      - id: sort-simple-yaml
+        files: '.yaml$'
+      - id: detect-private-key
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+      - id: black
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.3.1
+    hooks:
+      - id: remove-tabs
+        exclude: '(\.tsv|Makefile)$'
+      - id: remove-crlf

.travis.yml

@@ -1,16 +1,16 @@
-language: python
-python:
-  - 3.6
-  - 3.7
-  - 3.8
-before_install:
-  - python --version
-  - pip install -U pip
-  - pip install -U pytest
-  - pip install -U importlib_metadata
-  - pip install codecov
-install:
-  - pip install ".[test]" . # install package + test dependencies
-script: pytest # run tests
-after_success:
-  - codecov # submit coverage
+language: python
+python:
+  - 3.7
+  - 3.8
+  - 3.9
+before_install:
+  - python --version
+  - pip install -U pip
+  - pip install -U pytest
+  - pip install -U importlib_metadata
+  - pip install codecov
+install:
+  - pip install ".[test]" . # install package + test dependencies
+script: pytest # run tests
+after_success:
+  - codecov # submit coverage

README.rst

@@ -36,7 +36,7 @@ Installation
 ModelSEEDpy will soon be installable via the ``PyPI`` channel::
 
  pip install modelseedpy
- 
+
 but, until then, the repository must cloned::
 
  git clone https://github.com/ModelSEED/ModelSEEDpy.git
@@ -45,13 +45,13 @@ and then locally installed with ``pip``::
 
  cd path/to/modelseedpy
  pip install .
-   
+
 The associated ModelSEED Database, which is required for a few packages, is simply downloaded by cloning the GitHub repository::
 
  git clone https://github.com/ModelSEED/ModelSEEDDatabase.git
-   
-and the path to this repository is passed as an argument to the corresponding packages. 
-   
+
+and the path to this repository is passed as an argument to the corresponding packages.
+
 **Windows users** must separately install the ``pyeda`` module: 1) download the appropriate wheel for your Python version from `this website <https://www.lfd.uci.edu/~gohlke/pythonlibs/#pyeda>`_ ; and 2) install the wheel through the following commands in a command prompt/powershell console::
 
  cd path/to/pyeda/wheel

docs/index.rst

@@ -19,4 +19,3 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-