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 <[email protected]> * style: remove WARNING Co-authored-by: Moritz E. Beber <[email protected]> * fix: reconcile blocked with excluded reactions in OptKnock * chore: unpin optlang * chore: update pickles Co-authored-by: Jorge Carrasco <[email protected]> Co-authored-by: Moritz E. Beber <[email protected]>
biosustain · Oct 5, 2021 · 7f0e9d3 · 7f0e9d3
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,125 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+    - devel
+    tags:
+    - '[0-9]+.[0-9]+.[0-9]+'
+    - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
+  pull_request:
+    branches:
+    - master
+    - devel
+  schedule:
+  # https://crontab.guru/#0_8_1_*_*
+  - cron: '0 8 1 * *'
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # consider using these
+        # os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt install openbabel
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install tox tox-gh-actions
+    - name: Install CPLEX (when supported)
+      env:
+        CPLEX_SECRET: ${{ secrets.CPLEX_SECRET }}
+        PYTHON_VERSION: ${{ matrix.python-version }}
+      shell: bash
+      run: ./scripts/install_cplex.sh
+    - name: Test with tox
+      run:
+        tox -- --cov-report=xml
+    - name: Report coverage
+      shell: bash
+      run: bash <(curl -s https://codecov.io/bash)
+
+  release:
+    needs: test
+    if: startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get tag
+      id: tag
+      run: echo "::set-output name=version::${GITHUB_REF#refs/tags/}"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install twine
+    - name: Build package
+      run: python setup.py sdist bdist_wheel
+    - name: Check the package
+      run: twine check dist/*
+    - name: Publish to PyPI
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run:
+        twine upload --skip-existing --non-interactive dist/*
+    - name: Create GitHub release
+      uses: actions/create-release@v1
+      env:
+        # This token is set by gh actions
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ github.ref }}
+        release_name: ${{ github.ref }}
+        body_path: "release-notes/${{ steps.tag.outputs.version }}.md"
+        draft: false
+        prerelease: false
+
+  deploy-docs:
+    needs: test
+    if: startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      # TODO: consider pip cache
+      run: |
+        sudo apt-get install pandoc swig
+        python3 -m pip install ".[docs,jupyter]"
+    - name: Build docs
+      run: cd docs && make apidoc && make html && touch _build/html/.nojekyll
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build/html
+        cname: cameo.bio
diff --git a/.travis.yml b/.travis.yml
diff --git a/.travis/install_cplex.sh b/.travis/install_cplex.sh
diff --git a/README.rst b/README.rst
@@ -4,7 +4,7 @@ Cameo—Computer Aided Metabolic Engineering and Optimization
 .. summary-start
 
 |Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|
-|Build Status| |Coverage Status| |DOI| |zenhub|
+|Build Status| |Coverage Status| |DOI| |zenhub| |binder|
 
 What is cameo?
 ~~~~~~~~~~~~~~
@@ -141,3 +141,5 @@ Contributions
    :target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo
 .. |zenhub| image:: https://img.shields.io/badge/Shipping_faster_with-ZenHub-5e60ba.svg?style=flat-square
    :target: https://zenhub.com
+.. |binder| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/biosustain/cameo-notebooks/binder?urlpath=lab/tree/index.ipynb
diff --git a/cameo/flux_analysis/simulation.py b/cameo/flux_analysis/simulation.py
@@ -518,9 +518,10 @@ def display_on_map(self, map_name=None, palette="YlGnBu"):
 
             if in_ipnb():
                 from IPython.display import display
-                display(builder.display_in_notebook())
+                display(builder)
             else:
-                builder.display_in_browser()
+                logger.info(f"Escher Map generated at {map_name}.html")
+                builder.save_html(f"{map_name}.html")
 
         except ImportError:
             print("Escher must be installed in order to visualize maps")

diff --git a/cameo/strain_design/deterministic/flux_variability_based.py b/cameo/strain_design/deterministic/flux_variability_based.py
@@ -77,7 +77,7 @@ class DifferentialFVA(StrainDesignMethod):
 
     Compares flux ranges of a reference model to a set of models that
     have been parameterized to lie on a grid of evenly spaced points in the
-    n-dimensional production envelope (n being the number of reaction bounds
+    # n-dimensional production envelope (n being the number of reaction bounds
     to be varied).
     ::
         production
@@ -626,9 +626,22 @@ def nth_panel(self, index):
         """
         return self.groups.get_group(sorted(self.groups.groups.keys())[index]).copy()
 
-    def plot(self, index=None, variables=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
+    def plot(
+        self,
+        plotter,
+        index=None,
+        variables=None,
+        grid=None,
+        width=None,
+        height=None,
+        title=None,
+        palette=None,
+        **kwargs
+    ):
         if index is not None:
-            self._plot_flux_variability_analysis(index, variables=variables, width=width, grid=grid, palette=palette)
+            self._plot_flux_variability_analysis(
+                plotter, index, variables=variables, width=width, grid=grid, palette=palette
+            )
         else:
             self._plot_production_envelope(title=title, grid=grid, width=width, height=height)
 
@@ -768,9 +781,10 @@ def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
 
             if in_ipnb():
                 from IPython.display import display
-                display(builder.display_in_notebook())
+                display(builder)
             else:
-                builder.display_in_browser()
+                logger.info(f"Escher Map generated at {map_name}.html")
+                builder.save_html(f"{map_name}.html")
 
         except ImportError:
             print("Escher must be installed in order to visualize maps")
@@ -821,7 +835,7 @@ def _init_builder(self, reaction_data, objective, variable):
                                            dict(type='min', color="red", size=20),
                                            dict(type='median', color="grey", size=7),
                                            dict(type='max', color='green', size=20)], **self.kwargs_for_escher)
-        display(self.builder.display_in_notebook())
+        display(self.builder)
 
 
 class _DifferentialFvaEvaluator(object):
@@ -848,7 +862,7 @@ def _set_bounds(self, point):
             reaction.upper_bound = reaction.lower_bound = bound
         target_reaction = self.model.reactions.get_by_id(self.objective)
         target_bound = point[self.objective]
-        target_reaction.upper_bound = target_reaction.lower_bound = target_bound
+        target_reaction.bounds = (target_bound, target_bound)
 
 
 class FSEOF(StrainDesignMethod):
@@ -964,10 +978,9 @@ def run(self, target=None, max_enforced_flux=0.9, number_of_results=10, exclude=
             results = {reaction.id: [] for reaction in model.reactions}
 
             for level in levels:
-                target.lower_bound = level
-                target.upper_bound = level
+                target.bounds = (level, level)
                 solution = simulation_method(model, **simulation_kwargs)
-                for reaction_id, flux in solution.fluxes.iteritems():
+                for reaction_id, flux in solution.fluxes.items():
                     results[reaction_id].append(round(flux, ndecimals))
 
         # Test each reaction

diff --git a/cameo/strain_design/deterministic/linear_programming.py b/cameo/strain_design/deterministic/linear_programming.py
@@ -120,13 +120,16 @@ def __init__(self, model, exclude_reactions=None, remove_blocked=True, fraction_
 
         if fraction_of_optimum is not None:
             fix_objective_as_constraint(self._model, fraction=fraction_of_optimum)
-        if remove_blocked:
-            self._remove_blocked_reactions()
+        blocked = self._remove_blocked_reactions() if remove_blocked else []
         if exclude_reactions:
             # Convert exclude_reactions to reaction ID's
             exclude_reactions = [
-                r.id if isinstance(r, cobra.core.Reaction) else r for r in exclude_reactions
+                r.id if isinstance(r, cobra.core.Reaction) else r
+                for r in exclude_reactions
             ]
+            # if a blocked reaction were in exclude reactions, it would raise
+            # because blocked reactions are removed from the model
+            exclude_reactions = [r_id for r_id in exclude_reactions if r_id not in blocked]
             for r_id in exclude_reactions:
                 if r_id not in self._model.reactions:
                     raise ValueError("Excluded reaction {} is not in the model".format(r_id))
@@ -139,13 +142,13 @@ def __init__(self, model, exclude_reactions=None, remove_blocked=True, fraction_
 
     def _remove_blocked_reactions(self):
         fva_res = flux_variability_analysis(self._model, fraction_of_optimum=0)
-        # FIXME: Iterate over the index only (reaction identifiers).
         blocked = [
-            self._model.reactions.get_by_id(reaction) for reaction, row in fva_res.data_frame.iterrows()
+            reaction for reaction, row in fva_res.data_frame.iterrows()
             if (round(row["lower_bound"], config.ndecimals) == round(
                 row["upper_bound"], config.ndecimals) == 0)
         ]
         self._model.remove_reactions(blocked)
+        return blocked
 
     def _reduce_to_nullspace(self, reactions):
         self.reaction_groups = find_coupled_reactions_nullspace(self._model)

diff --git a/cameo/visualization/escher_ext.py b/cameo/visualization/escher_ext.py
@@ -99,4 +99,4 @@ def _draw_js(self, the_id, enable_editing, menu, enable_keys, dev,
         return draw
 
     def _repr_html_(self):
-        return self.display_in_notebook()
+        return display(self)