Draft: Update pituitary gland ODE with better simulator, ODE class and dataframe

.bumpversion.cfg

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+[bumpversion]
+current_version = 0.2.0.dev0
+commit = True
+tag = False
+files = traja/__init__.py
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<n>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{release}{n}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = post
+first_value = dev
+values = 
+	dev
+	post
+
+[bumpversion:part:n]
+

.coveragerc

@@ -0,0 +1,10 @@
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError
+    if __name__ == .__main__.:
+omit =
+    traja/tests/*
+    traja/contrib/*

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 120
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.github/workflows/draft-pdf.yml

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+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/tests.yaml

@@ -0,0 +1,54 @@
+name: Tests
+
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  pull_request:
+    branches: [master]
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest", "windows-latest"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          channels: conda-forge,defaults
+          environment-file: environment.yml
+          python-version: 3.8
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8
+            python -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+            python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            pip install -r requirements/dev.txt
+            pip install -r requirements/docs.txt
+            pip install --upgrade pytest flake8 sphinx
+            pip install scipy --force-reinstall # for https://github.com/conda/conda/issues/6396
+            pip install .
+            conda install pytest
+            py.test . --cov-report=xml --cov=traja
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          verbose: false

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+.DS_Store
+
+# Visualstudio code file
+.vscode
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.idea
+
+_build/
+
+# BUILD FILES
+*.zip
+hypers.json
+model
+
+docs/source/gallery
+docs/source/savefig
+docs/source/reference
+
+# Editor files
+*.swp
+*.swo
+
+
+# Model parameter files
+*.pt

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.7
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+    -   id: flake8
+        language: python_venv

.readthedocs.yml

@@ -0,0 +1,13 @@
+version: 2
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+build:
+  image: latest
+
+python:
+  version: 3.7
+  install:
+    - requirements: requirements/docs.txt

.travis.yml

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+sudo: false
+
+dist: xenial
+
+language: python
+
+python:
+ - '3.7'
+ - '3.8'
+
+git:
+  depth: false
+
+env:
+ - MPLBACKEND=Agg CODECOV_TOKEN="287389e5-8f99-42e1-8844-17acef7c454f"
+
+cache: pip
+
+before_install:
+  - sudo apt-get update
+
+install:
+- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  -O miniconda.sh
+- bash miniconda.sh -b -p $HOME/miniconda
+- export PATH="$HOME/miniconda/bin:$PATH"
+- hash -r
+- conda config --set always_yes yes --set changeps1 no
+- conda update -q conda
+- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION 
+- source activate test-environment
+- pip install -r requirements/dev.txt
+- pip install -r requirements/docs.txt
+- pip install --upgrade pytest flake8 sphinx
+- pip install .
+script:
+ - cd docs && make doctest && cd ..
+ - py.test . --cov-report term --cov=traja
+
+after_success:
+ - codecov
+
+deploy:
+  provider: pypi
+  user: jshenk
+  skip_cleanup: true
+  skip_existing: true
+  on:
+    tags: true
+    branch: master
+  password:
+    secure: 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

CITATION

@@ -0,0 +1,11 @@
+@software{justin_shenk_2019_3237827,
+  author       = {Justin Shenk and
+                  the Traja development team},
+  title        = {justinshenk/traja},
+  month        = jun,
+  year         = 2019,
+  publisher    = {Zenodo},
+  version      = {latest},
+  doi          = {10.5281/zenodo.3237827},
+  url          = {https://doi.org/10.5281/zenodo.3237827}
+}

LICENSE

@@ -0,0 +1,7 @@
+Copyright 2019 Justin Shenk
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.