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phantomas1234carrascomjMidnighter
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Merge devel into master (#284)
* Replace Travis with github actions (#270) * chore: replace travis with gh actions * test: replace TRAVIS env var with CI * test: run CI only linux for now * chore: add release gh action * docs: add docs gh action * fix: get syntax and deps right * chore: merge docs with release action * fix: install openbabel on CI * refactor: merge release and main actions * fix: use secrets for publishing to pypi * chore: install CPLEX on CI py3.6 * fix: typo * fix: extract cplex properly * chore: schedule CI run every month * Fix plotting (#272) * fix: update escher everywhere * docs: explain how to work in jupyterlab * style: apply flake8 * docs: format missing code block properly * fix: remove docstring typo * Refactor bounds behaviour (#273) * fix: update escher everywhere * docs: explain how to work in jupyterlab * style: apply flake8 * docs: format missing code block properly * refactor: adopt new bounds behavior opencobra/cobrapy#793 * style: improve readability * docs: add badge to binder (#274) * Docs enhance (#276) * fix: update escher everywhere * docs: explain how to work in jupyterlab * style: apply flake8 * docs: format missing code block properly * docs: show favicon * docs: regenerate tutorial notebooks * style: use :py: in API links Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * style: remove WARNING Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * fix: reconcile blocked with excluded reactions in OptKnock * chore: unpin optlang * chore: update pickles Co-authored-by: Jorge Carrasco <carrascomurielj@gmail.com> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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‎.github/workflows/main.yml‎

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name: CI
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on:
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push:
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branches:
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- master
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- devel
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tags:
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- '[0-9]+.[0-9]+.[0-9]+'
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- '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
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pull_request:
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branches:
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- master
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- devel
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schedule:
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# https://crontab.guru/#0_8_1_*_*
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- cron: '0 8 1 * *'
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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# consider using these
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# os: [ubuntu-latest, macos-latest, windows-latest]
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os: [ubuntu-latest]
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python-version: [3.6, 3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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sudo apt install openbabel
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install tox tox-gh-actions
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- name: Install CPLEX (when supported)
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env:
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CPLEX_SECRET: ${{ secrets.CPLEX_SECRET }}
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PYTHON_VERSION: ${{ matrix.python-version }}
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shell: bash
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run: ./scripts/install_cplex.sh
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- name: Test with tox
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run:
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tox -- --cov-report=xml
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- name: Report coverage
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shell: bash
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run: bash <(curl -s https://codecov.io/bash)
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release:
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needs: test
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if: startsWith(github.ref, 'refs/tags')
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get tag
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id: tag
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run: echo "::set-output name=version::${GITHUB_REF#refs/tags/}"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install twine
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- name: Build package
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run: python setup.py sdist bdist_wheel
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- name: Check the package
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run: twine check dist/*
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- name: Publish to PyPI
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run:
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twine upload --skip-existing --non-interactive dist/*
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- name: Create GitHub release
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uses: actions/create-release@v1
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env:
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# This token is set by gh actions
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ github.ref }}
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release_name: ${{ github.ref }}
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body_path: "release-notes/${{ steps.tag.outputs.version }}.md"
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draft: false
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prerelease: false
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deploy-docs:
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needs: test
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if: startsWith(github.ref, 'refs/tags')
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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# TODO: consider pip cache
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run: |
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sudo apt-get install pandoc swig
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python3 -m pip install ".[docs,jupyter]"
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- name: Build docs
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run: cd docs && make apidoc && make html && touch _build/html/.nojekyll
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/_build/html
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cname: cameo.bio

‎.travis.yml‎

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‎.travis/install_cplex.sh‎

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‎README.rst‎

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@@ -4,7 +4,7 @@ Cameo—Computer Aided Metabolic Engineering and Optimization
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.. summary-start
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|Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|
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|Build Status| |Coverage Status| |DOI| |zenhub|
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|Build Status| |Coverage Status| |DOI| |zenhub| |binder|
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What is cameo?
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~~~~~~~~~~~~~~
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:target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo
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.. |zenhub| image:: https://img.shields.io/badge/Shipping_faster_with-ZenHub-5e60ba.svg?style=flat-square
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:target: https://zenhub.com
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.. |binder| image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/biosustain/cameo-notebooks/binder?urlpath=lab/tree/index.ipynb

‎cameo/flux_analysis/simulation.py‎

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@@ -518,9 +518,10 @@ def display_on_map(self, map_name=None, palette="YlGnBu"):
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if in_ipnb():
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from IPython.display import display
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display(builder.display_in_notebook())
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display(builder)
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else:
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builder.display_in_browser()
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logger.info(f"Escher Map generated at {map_name}.html")
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builder.save_html(f"{map_name}.html")
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except ImportError:
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print("Escher must be installed in order to visualize maps")

‎cameo/strain_design/deterministic/flux_variability_based.py‎

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@@ -77,7 +77,7 @@ class DifferentialFVA(StrainDesignMethod):
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Compares flux ranges of a reference model to a set of models that
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have been parameterized to lie on a grid of evenly spaced points in the
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n-dimensional production envelope (n being the number of reaction bounds
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# n-dimensional production envelope (n being the number of reaction bounds
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to be varied).
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::
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production
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"""
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return self.groups.get_group(sorted(self.groups.groups.keys())[index]).copy()
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def plot(self, index=None, variables=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
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def plot(
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self,
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plotter,
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index=None,
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variables=None,
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grid=None,
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width=None,
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height=None,
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title=None,
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palette=None,
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**kwargs
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):
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if index is not None:
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self._plot_flux_variability_analysis(index, variables=variables, width=width, grid=grid, palette=palette)
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self._plot_flux_variability_analysis(
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plotter, index, variables=variables, width=width, grid=grid, palette=palette
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)
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else:
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self._plot_production_envelope(title=title, grid=grid, width=width, height=height)
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if in_ipnb():
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from IPython.display import display
771-
display(builder.display_in_notebook())
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display(builder)
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else:
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builder.display_in_browser()
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logger.info(f"Escher Map generated at {map_name}.html")
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builder.save_html(f"{map_name}.html")
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except ImportError:
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print("Escher must be installed in order to visualize maps")
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dict(type='min', color="red", size=20),
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dict(type='max', color='green', size=20)], **self.kwargs_for_escher)
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display(self.builder.display_in_notebook())
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display(self.builder)
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class _DifferentialFvaEvaluator(object):
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reaction.upper_bound = reaction.lower_bound = bound
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target_reaction = self.model.reactions.get_by_id(self.objective)
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target_bound = point[self.objective]
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target_reaction.upper_bound = target_reaction.lower_bound = target_bound
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target_reaction.bounds = (target_bound, target_bound)
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class FSEOF(StrainDesignMethod):
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results = {reaction.id: [] for reaction in model.reactions}
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for level in levels:
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target.lower_bound = level
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target.upper_bound = level
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target.bounds = (level, level)
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solution = simulation_method(model, **simulation_kwargs)
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for reaction_id, flux in solution.fluxes.iteritems():
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for reaction_id, flux in solution.fluxes.items():
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results[reaction_id].append(round(flux, ndecimals))
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# Test each reaction

‎cameo/strain_design/deterministic/linear_programming.py‎

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if fraction_of_optimum is not None:
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fix_objective_as_constraint(self._model, fraction=fraction_of_optimum)
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if remove_blocked:
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self._remove_blocked_reactions()
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blocked = self._remove_blocked_reactions() if remove_blocked else []
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if exclude_reactions:
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# Convert exclude_reactions to reaction ID's
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exclude_reactions = [
128-
r.id if isinstance(r, cobra.core.Reaction) else r for r in exclude_reactions
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r.id if isinstance(r, cobra.core.Reaction) else r
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for r in exclude_reactions
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]
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# if a blocked reaction were in exclude reactions, it would raise
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# because blocked reactions are removed from the model
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exclude_reactions = [r_id for r_id in exclude_reactions if r_id not in blocked]
130133
for r_id in exclude_reactions:
131134
if r_id not in self._model.reactions:
132135
raise ValueError("Excluded reaction {} is not in the model".format(r_id))
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def _remove_blocked_reactions(self):
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# FIXME: Iterate over the index only (reaction identifiers).
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blocked = [
144-
self._model.reactions.get_by_id(reaction) for reaction, row in fva_res.data_frame.iterrows()
146+
reaction for reaction, row in fva_res.data_frame.iterrows()
145147
if (round(row["lower_bound"], config.ndecimals) == round(
146148
row["upper_bound"], config.ndecimals) == 0)
147149
]
148150
self._model.remove_reactions(blocked)
151+
return blocked
149152

150153
def _reduce_to_nullspace(self, reactions):
151154
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‎cameo/visualization/escher_ext.py‎

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return draw
100100

101101
def _repr_html_(self):
102-
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102+
return display(self)

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