Merge branch 'main' into stable

Author: guillaume-gricourt

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
      tag: ${{ steps.tag_label.outputs.tag }}
      changelog: ${{ steps.tag_raw.outputs.changelog }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -36,7 +36,7 @@ jobs:
   Changelog:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -57,7 +57,7 @@ jobs:
           echo "$USER $PROJECT"
           github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
       - name: 'Upload Artifact Changelog'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: changelog-artifact
           path: CHANGELOG.md
@@ -70,7 +70,7 @@ jobs:
       version_path: ${{ steps.update_version.outputs.version_path }}
       version_dir: ${{ steps.update_version.outputs.version_dir }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: 'Update _version.py'
         id: update_version
         env:
@@ -82,7 +82,7 @@ jobs:
           echo "version_path=$VERSION_PATH" >> "$GITHUB_OUTPUT"
           echo "version_dir=$VERSION_DIR" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Version'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: version-artifact
           path: ${{ steps.update_version.outputs.version_path }}
@@ -93,17 +93,17 @@ jobs:
     steps:
       # Get Data
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
       - name: 'Download Artifact Version'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: version-artifact
           path: ${{ needs.Version.outputs.version_dir }}
       - name: 'Download Artifact Changelog'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: changelog-artifact
       # Commit
@@ -133,7 +133,7 @@ jobs:
     needs: [Commit, TagRaw]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -158,9 +158,9 @@ jobs:
         shell: bash -l {0} # activate env conda
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
@@ -178,7 +178,7 @@ jobs:
           filename=$(find ${{ env.dirbuild }} | head -n 1)
           echo "asset=$filename" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Package'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: package-conda-artifact
           path: ${{ steps.identify_asset.outputs.asset }}
@@ -190,7 +190,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Download Artifact Package - Pip'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: package-conda-artifact
       - name: 'Create Release'

.github/workflows/lint.yml

@@ -8,12 +8,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
           fetch-depth: 0
       - name: Lint Code Base
-        uses: github/super-linter@v4
+        uses: github/super-linter@v5
         env:
           VALIDATE_ALL_CODEBASE: false
           VALIDATE_YAML: false

.github/workflows/test.yml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches:
       - main
+  schedule:
+    - cron: '0 0 * * 1'
 
 jobs:
 
@@ -17,11 +19,11 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
       - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
@@ -44,11 +46,11 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
       - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
@@ -70,11 +72,11 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
       - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## [3.2.1](https://github.com/brsynth/straindesign/tree/3.2.1) (2023-01-23)
+
+[Full Changelog](https://github.com/brsynth/straindesign/compare/3.2.0...3.2.1)
+
+**Merged pull requests:**
+
+- chore\(deps\): bump mathieudutour/github-tag-action from 6.0 to 6.1 [\#6](https://github.com/brsynth/straindesign/pull/6) ([dependabot[bot]](https://github.com/apps/dependabot))
+- chore\(deps\): bump actions/upload-artifact from 2 to 3 [\#5](https://github.com/brsynth/straindesign/pull/5) ([dependabot[bot]](https://github.com/apps/dependabot))
+
 ## [3.2.0](https://github.com/brsynth/straindesign/tree/3.2.0) (2023-01-05)
 
 [Full Changelog](https://github.com/brsynth/straindesign/compare/3.1.0...3.2.0)

recipes/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "straindesign" %}
-{% set version = "3.1.0" %}
+{% set version = "3.2.3" %}
 
 package:
   name: {{ name }}
@@ -16,29 +16,25 @@ build:
 requirements:
   build:
     - pip
-    - python
+    - python>=3.8
     - pyyaml
     - setuptools
   run:
     - biopython
     - blessings
-    - click
-    - cobra>=0.24
+    - cobra>=0.29
     - escher
     - future
     - gnomic
     - inspyred
     - IProgress
     - lazy-object-proxy
     - plotly
-    - python
-    - markupsafe
+    - python>=3.8
     - networkx
     - numexpr
-    - numpy<1.24 # Related to https://github.com/numpy/numpy/pull/22607
     - openbabel
     - openpyxl
-    - optlang
     - ordered-set
     - palettable
     - pandas

recipes/workflow.yaml

@@ -1,4 +1,4 @@
-name: test
+name: straindesign-local
 channels:
   - conda-forge
   - plotly
@@ -8,7 +8,7 @@ dependencies:
   - biopython
   - blessings
   - click
-  - cobra>=0.24
+  - cobra
   - conda-build
   - escher
   - future
@@ -20,10 +20,9 @@ dependencies:
   - markupsafe
   - networkx
   - numexpr
-  - numpy<1.24 # Related to https://github.com/numpy/numpy/pull/22607
+  - numpy
   - openbabel
   - openpyxl
-  - optlang
   - ordered-set
   - palettable
   - pandas

src/cameobrs/strain_design/deterministic/flux_variability_based.py

@@ -360,11 +360,7 @@ def run(
         ].values
 
         if self.normalize_ranges_by is not None:
-            logger.debug(
-                self.reference_flux_ranges.loc[
-                    self.normalize_ranges_by,
-                ]
-            )
+            logger.debug(self.reference_flux_ranges.loc[self.normalize_ranges_by,])
             # The most obvious flux to normalize by is the biomass reaction
             # flux. This is probably always greater than zero. Just in case
             # the model is defined differently or some other normalizing
@@ -435,7 +431,7 @@ def run(
                 results = list(view.map(func_obj, self.grid.iterrows()))
 
         solutions = dict(
-            (tuple(point.iteritems()), fva_result) for (point, fva_result) in results
+            (tuple(point.items()), fva_result) for (point, fva_result) in results
         )
 
         for sol in solutions.values():
@@ -880,7 +876,7 @@ def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
             reaction_data[numpy.isposinf(reaction_data)] = reaction_data.max()
             reaction_data[numpy.isneginf(reaction_data)] = reaction_data.min()
 
-            reaction_data = dict(reaction_data.iteritems())
+            reaction_data = dict(reaction_data.items())
             reaction_data["max"] = numpy.abs(values).max()
             reaction_data["min"] = -reaction_data["max"]
 
@@ -1114,7 +1110,6 @@ def run(
                 exclude_ids.append(reaction)
 
         with TimeMachine() as tm:
-
             tm(do=int, undo=partial(setattr, model, "objective", model.objective))
             tm(do=int, undo=partial(setattr, target, "lower_bound", target.lower_bound))
             tm(do=int, undo=partial(setattr, target, "upper_bound", target.upper_bound))
@@ -1228,7 +1223,6 @@ def __init__(
         *args,
         **kwargs,
     ):
-
         super(FSEOFResult, self).__init__(
             self._generate_designs(reference, enforced_levels, reaction_results),
             *args,

src/straindesign/_version.py

@@ -1,2 +1,2 @@
 __app_name__ = "straindesign"
-__version__ = "3.2.1"
+__version__ = "3.2.2"

tests/cameobrs/unit/test_strain_design_deterministic.py

@@ -207,11 +207,11 @@ def test_result_is_correct(self, glpk_growth_coupling_potential):
         fva = cameobrs.flux_variability_analysis(
             model, fraction_of_optimum=1, remove_cycles=False, reactions=["PFL"]
         )
-        assert fva["lower_bound"][0] <= 0 <= fva["upper_bound"][0]
+        assert fva["lower_bound"].iloc[0] <= 0 <= fva["upper_bound"].iloc[0]
         with model:
             for knockout in knockouts:
                 model.reactions.get_by_id(knockout).knock_out()
             fva = cameobrs.flux_variability_analysis(
                 model, fraction_of_optimum=1, remove_cycles=False, reactions=["PFL"]
             )
-            assert abs(fva["lower_bound"][0]) > 4
+            assert abs(fva["lower_bound"].iloc[0]) > 4