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

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

.flake8

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

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.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

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+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 -vvv
+      - 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

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+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

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+@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}
+}