Merge branch 'cshenry-main'

freiburgermsu · Aug 29, 2024 · 2dfeb68 · 2dfeb68
2 parents 937829d + cca64e5
commit 2dfeb68
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diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -1,25 +1,27 @@
-name: Run Pre-Commit
-
-on:
-  pull_request: {}
-  push:
-    branches:
-      - dev
-      - main
-
-jobs:
-  pre-commit:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10']
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Set file mode to false
-        run: |
-          git config core.filemode false
-      - uses: pre-commit/action@v2.0.3
+name: Run Pre-Commit
+
+on:
+  pull_request: {}
+  push:
+    paths-ignore:
+      - 'examples/**'
+    branches:
+      - dev
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.8', '3.9', '3.10']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set file mode to false
+        run: |
+          git config core.filemode false
+      - uses: pre-commit/action@v2.0.3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,42 +1,44 @@
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-      - id: fix-encoding-pragma
-      - id: check-merge-conflict
-      - id: end-of-file-fixer
-      - id: debug-statements
-      - id: check-added-large-files
-      - id: check-ast
-      - id: check-byte-order-marker
-      - id: check-case-conflict
-      - id: check-docstring-first
-      - id: check-executables-have-shebangs
-        types: [python]
-      - id: check-vcs-permalinks
-      - id: check-symlinks
-      - id: mixed-line-ending
-      - id: name-tests-test
-        exclude: tests/test_data
-        args:
-          - --pytest-test-first
-      - id: check-json
-      - id: pretty-format-json
-        args:
-          - --autofix
-          - --top-keys=_id
-      - id: check-yaml
-      - id: sort-simple-yaml
-        files: '.yaml$'
-      - id: detect-private-key
-      - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 22.8.0
-    hooks:
-      - id: black
-  - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.3.1
-    hooks:
-      - id: remove-tabs
-        exclude: '(\.tsv|Makefile)$'
-      - id: remove-crlf
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: fix-encoding-pragma
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: debug-statements
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-byte-order-marker
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+        types: [python]
+      - id: check-vcs-permalinks
+      - id: check-symlinks
+      - id: mixed-line-ending
+      - id: name-tests-test
+        exclude: tests/test_data
+        args:
+          - --pytest-test-first
+      - id: check-json
+        exclude: examples/
+      - id: pretty-format-json
+        exclude: examples/
+        args:
+          - --autofix
+          - --top-keys=_id
+      - id: check-yaml
+      - id: sort-simple-yaml
+        files: '.yaml$'
+      - id: detect-private-key
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+      - id: black
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.3.1
+    hooks:
+      - id: remove-tabs
+        exclude: '(\.tsv|Makefile)$'
+      - id: remove-crlf
diff --git a/examples/Model Reconstruction/ATPGapfilling.ipynb b/examples/Model Reconstruction/ATPGapfilling.ipynb
diff --git a/modelseedpy/__init__.py b/modelseedpy/__init__.py
@@ -1,54 +1,66 @@
-# -*- coding: utf-8 -*-
-
-from __future__ import absolute_import
-
-# set the warning format to be on a single line
-import sys
-import logging
-import cobra
-import warnings as _warnings
-from os import name as _name
-from os.path import abspath as _abspath
-from os.path import dirname as _dirname
-from modelseedpy.helpers import config
-
-__author__ = "Christopher Henry"
-__email__ = "chenry@anl.gov"
-__version__ = "0.2.2"
-
-logger = logging.getLogger(__name__)
-
-print("modelseedpy", __version__)
-
-if sys.version_info[0] == 2:
-    logger.warning(
-        "Python 2 is reaching end of life (see "
-        "https://www.python.org/dev/peps/pep-0373/) and many cobra "
-        "dependencies have already dropped support. At the moment it *should* "
-        "still work but we will no longer actively maintain Python 2 support."
-    )
-
-if "e0" not in cobra.medium.annotations.compartment_shortlist["e"]:
-    cobra.medium.annotations.compartment_shortlist["e"].append("e0")
-
-import modelseedpy
-from modelseedpy.core import (
-    RastClient, MSGenome, MSBuilder, MSMedia, MSGrowthPhenotypes, MSModelUtil,
-    FBAHelper, MSEditorAPI, MSATPCorrection, MSGapfill, MSEquation, OptlangHelper,
-    commscores_report, steadycom_report
-)
-from modelseedpy.core.exceptions import *
-
-from modelseedpy.community import (
-    MSCommunity, CommunityMember, MSKineticsFBA, CommPhitting,
-    MSSteadyCom, build_from_species_models, phenotypes)
-
-from modelseedpy.biochem import ModelSEEDBiochem
-
-from modelseedpy.fbapkg import (
-    BaseFBAPkg, RevBinPkg, ReactionUsePkg, SimpleThermoPkg, TotalFluxPkg, BilevelPkg, CommKineticPkg,
-    KBaseMediaPkg, FluxFittingPkg, ProteomeFittingPkg, GapfillingPkg, MetaboFBAPkg, FlexibleBiomassPkg,
-    ProblemReplicationPkg, FullThermoPkg, MSPackageManager, ObjConstPkg, ChangeOptPkg, ElementUptakePkg
-)
-
-from modelseedpy.multiomics import MSExpression
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+# set the warning format to be on a single line
+import sys
+import logging
+import cobra
+import warnings as _warnings
+from os import name as _name
+from os.path import abspath as _abspath
+from os.path import dirname as _dirname
+from modelseedpy.helpers import config
+
+__author__ = "Christopher Henry"
+__email__ = "chenry@anl.gov"
+__version__ = "0.3.3"
+
+logger = logging.getLogger(__name__)
+
+print("modelseedpy", __version__)
+
+if sys.version_info[0] == 2:
+    logger.warning(
+        "Python 2 is reaching end of life (see "
+        "https://www.python.org/dev/peps/pep-0373/) and many cobra "
+        "dependencies have already dropped support. At the moment it *should* "
+        "still work but we will no longer actively maintain Python 2 support."
+    )
+
+if "e0" not in cobra.medium.annotations.compartment_shortlist["e"]:
+    cobra.medium.annotations.compartment_shortlist["e"].append("e0")
+
+import modelseedpy
+from modelseedpy.core import (
+    RastClient,
+    MSGenome,
+    MSBuilder,
+    MSMedia,
+    MSGrowthPhenotypes,
+    MSGrowthPhenotype,
+    MSModelUtil,
+    FBAHelper,
+    MSEditorAPI,
+    MSATPCorrection,
+    MSGapfill,
+    MSEquation,
+    MSModelReport,
+    AnnotationOntology,
+    OptlangHelper
+)
+from modelseedpy.core.exceptions import *
+
+from modelseedpy.community import (
+    MSCommunity, CommunityMember, MSKineticsFBA, CommPhitting,
+    MSSteadyCom, build_from_species_models, phenotypes)
+
+from modelseedpy.biochem import ModelSEEDBiochem
+
+from modelseedpy.fbapkg import (
+    BaseFBAPkg, RevBinPkg, ReactionUsePkg, SimpleThermoPkg, TotalFluxPkg, BilevelPkg, CommKineticPkg,
+    KBaseMediaPkg, FluxFittingPkg, ProteomeFittingPkg, GapfillingPkg, MetaboFBAPkg, FlexibleBiomassPkg,
+    ProblemReplicationPkg, FullThermoPkg, MSPackageManager, ObjConstPkg, ChangeOptPkg, ElementUptakePkg
+)
+
+from modelseedpy.multiomics import MSExpression