Version 1.2.0 (#53)

Added: Memote example files added to docs Curation and visualization logs are now separated by date in a 'logs' dir Usage of credentials for BioCyc database New structure cobramod.retrieval.Data. It is in charge of parsing into different objects Extra functions in utils Changed: Set object bug fixed [#50] Escher is an optional dependency Pre-hooks uses now ruff instead of flake8 and black. Behaviour to open files if escher is not installed changed to not open browsers Dropped support for python 3.8 and 3.9 Logging format is more human-friendly Dropped support of mypy. Black is replaced with ruff New pyproject.toml Test data updated (19.02.24) Function available_databases replaced by cobramod.retrieval.Databases Structure for retrieval refactored and new parsing sub-packaged created DataVersion moved to parsing package Updated structure of test module Removed multiple "private" methods and functions. Docs files updated to these new changes Test updated to uses new changes Updating functions to not use deprecated pandas functions Removed: Deprecated config files Deprecation warning for SolCyc (Database appears to be shutdown)
Toepfer-Lab · Feb 20, 2024 · 4295766 · 4295766
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diff --git a/.github/workflows/test-build-and-publish.yml b/.github/workflows/test-build-and-publish.yml
@@ -11,67 +11,48 @@ on:
       - master
 
 jobs:
-  lint-format:
+  lint-format-unittest:
     runs-on: ubuntu-latest
     steps:
-        - uses: actions/checkout@v2
-        - uses: actions/setup-python@v2
-          with:
-            python-version: 3.7
-        - name: Install dependencies
-          run: python -m pip install tox
-        - name: Linter
-          run: python -m tox -e lint
-        - name: Format
-          run: python -m tox -e format
+      - uses: actions/checkout@v4
 
-  types:
-    needs: [lint-format]
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [ 3.7, 3.8, 3.9 ]
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install dependencies
-        run: python -m pip install tox
-      - name: Run type-checking
-        run: python -m tox -e types
-  test:
-    needs: [lint-format, types]
-    strategy:
-      matrix:
-        os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.7, 3.8, 3.9 ]
-    runs-on: ${{ matrix.os}}
-
-    steps:
-      - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
       - name: Install dependencies
-        run: python -m pip install tox
-      - name: Run tests
-        run: tox -e py
+        run: python -m pip install .
+
+      - name: Install tox
+        run: python -m pip install tox-gh>=1.2
+
+      - name: Setup test suite
+        run: tox -vv --notest
+
+      - name: Credentials
+        run: echo "${{ secrets.BIOCYC_USER }}\n${{ secrets.BIOCYC_PASS }}" >> credentials.txt
+
+      - name: Run test suite
+        run: tox --skip-pkg-install
 
   build-publish:
-    needs: [lint-format, types, test]
+    needs: [lint-format-unittest]
     name: Build and publish the package to TestPyPI
     if: github.event.pull_request.merged == true && github.event_name != 'schedule'
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.10
+        cache: "pip"
 
     - name: Install dependencies
       run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,23 +4,9 @@ repos:
     hooks:
     -   id: no-commit-to-branch
         args: [-b master]
--   repo: https://github.com/psf/black
-    rev: 19.3b0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.13
     hooks:
-    -   id: black
-        args: [--line-length=79, --check, --diff]
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.8
-    hooks:
-    -   id: flake8
-        args: [--config=.toml]
--   repo: https://github.com/pre-commit/mirrors-mypy.git
-    rev: v0.730
-    hooks:
-    -   id: mypy
-        args: [--config-file=mypy.ini]
--   repo: https://github.com/PyCQA/doc8
-    rev: 0.9.0a1
-    hooks:
-    -   id: doc8
-        arg: [--config=.toml]
+        - id: ruff
+        - id: ruff-format
+          args: [--config=pyproject.toml, --check]
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -4,7 +4,7 @@ conda:
   environment: environment.yml
 
 python:
-  version: 3.7
+  version: 3.10
   install:
     - method: pip
       path: .
diff --git a/.toml b/.toml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,46 @@
+# Changelog
+
+## [Unreleased]
+
+### Planned
+
+- Parallelization of downloads and cross-references
+- Visualization with other tools than Escher
+- Deprecation of SolCyc
+- Deprecation of PairDictionary
+
+## [1.2.0]
+
+### Added
+
+- Memote example files added to docs
+- Curation and visualization logs are now separated by date in a 'logs' dir
+- Usage of credentials for BioCyc database
+- New structure `cobramod.retrieval.Data`. It is in charge of parsing into
+  different objects
+- Extra functions in utils
+
+### Changed
+
+- Set object bug fixed [https://github.com/Toepfer-Lab/cobramod/issues/50]
+- Escher is an optional dependency
+- Pre-hooks uses now ruff instead of flake8 and black.
+- Behaviour to open files if escher is not installed changed to not open browsers
+- Dropped support for python 3.8 and 3.9
+- Logging format is more human-friendly
+- Dropped support of mypy. Black is replaced with ruff
+- New pyproject.toml
+- Test data updated (19.02.24)
+- Function `available_databases` replaced by `cobramod.retrieval.Databases`
+- Structure for retrieval refactored and new parsing sub-packaged created
+- DataVersion moved to parsing package
+- Updated structure of test module
+- Removed multiple "private" methods and functions. 
+- Docs files updated to these new changes
+- Test updated to uses new changes
+- Updating functions to not use deprecated pandas functions
+
+### Removed
+
+- Deprecated config files
+- Deprecation warning for SolCyc (Database appears to be shutdown)
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![Generic badge](https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9%20%7C%203.10-blue)
+![Static Badge](https://img.shields.io/badge/python-3.10%7C3.11%7C3.12-%20blue)
 ![GitHub](https://img.shields.io/github/license/Toepfer-Lab/cobramod)
 ![Read the Docs (version)](https://img.shields.io/readthedocs/cobramod/latest)
 ![Tests](https://img.shields.io/github/workflow/status/Toepfer-Lab/cobramod/Test%20build%20and%20publish%20Cobramod%20to%20PyPI?label=tests)
@@ -11,19 +11,17 @@ CobraMod: A pathway-centric curation tool for constraint-based metabolic models
 
 ![image](https://raw.githubusercontent.com/Toepfer-Lab/cobramod/master/docs/source/img/logo.png)
 
-CobraMod is a Python 3 open-source package for pathway-centric curation
-of genome-scale metabolic models (GEMs). It builds upon the [COBRApy
-toolbox](https://opencobra.github.io/cobrapy/) and offers a
-comprehensible set of functions for semi-automated network extension,
-curation and visualization. CobraMod supports all databases from the
-[BioCyc collection](https://biocyc.org/), the [KEGG
-database](https://www.genome.jp/kegg/), and the [BiGG Models
-repository](http://bigg.ucsd.edu/) and can directly interact with Escher
-for pathway and flux visualization.
+CobraMod is a Python 3 open-source package for pathway-centric curation of
+genome-scale metabolic models (GEMs). It builds upon the [COBRApy toolbox]
+(https://opencobra.github.io/cobrapy/) and offers a comprehensible set of
+functions for semi-automated network extension, curation and visualization.
+CobraMod supports all databases from the [BioCyc collection](https://
+biocyc.org/), the [KEGG database](https://www.genome.jp/kegg/), and the [BiGG
+Models repository](http://bigg.ucsd.edu/). It optionally can interact with
+Escher for pathway and flux visualization.
 
-This package converts pathway information into native COBRApy objects
-and quality-checks them while adding them to the model. This includes
-testing for:
+This package converts pathway information into native COBRApy objects and
+quality-checks them while adding them to the model. This includes testing for:
 
 -   duplicate elements
 -   correct chemical formula
@@ -34,9 +32,9 @@ testing for:
 -   MEMOTE compliance
 -   available cross-references
 
-CobraMod offers user-friendly tracking of the curation process with
-summary output and log files and customized pathway and flux
-visualization with [Escher](https://escher.github.io/).
+CobraMod offers user-friendly tracking of the curation process with summary
+output with log files and customized pathway and flux visualization with
+[Escher](https://escher.github.io/).
 
 Installation
 ------------
@@ -50,8 +48,7 @@ Functions
 
 This package offers multiple functions for modifying and extending GEMs:
 
--   Retrieve metabolic pathway information from a database
-    `cobramod.get_data`
+-   Retrieve metabolic pathway information from a database `cobramod.get_data`
 -   Transform stored data into COBRApy objects `cobramod.create_object`
 -   Add metabolites from multiple sources `cobramod.add_metabolites`
 -   Add reactions from multiple sources `cobramod.add_reactions`
@@ -73,15 +70,14 @@ To cite CobraMod, please use the following paper:
 
 ```bibtex
 @article{10.1093/bioinformatics/btac119,
-    author = {Camborda, Stefano and Weder, Jan-Niklas and Töpfer, Nadine},
+    author = {Camborda La Cruz, Stefano and Weder, Jan-Niklas and Töpfer, Nadine},
     title = "{CobraMod: a pathway-centric curation tool for constraint-based metabolic models}",
     journal = {Bioinformatics},
     volume = {38},
     number = {9},
     pages = {2654-2656},
     year = {2022},
     month = {02},
-    abstract = "{COnstraint-Based Reconstruction and Analysis of genome-scale metabolic models has become a widely used tool to understand metabolic network behavior at a large scale. However, existing reconstruction tools lack functionalities to address modellers' common objective to study metabolic networks on the pathway level. Thus, we developed CobraMod—a Python package for pathway-centric modification and extension of genome-scale metabolic networks. CobraMod can integrate data from various metabolic pathway databases as well as user-curated information. Our tool tests newly added metabolites, reactions and pathways against multiple curation criteria, suggests manual curation steps and provides the user with records of changes to ensure high quality metabolic reconstructions. CobraMod uses the visualization tool Escher for pathway representation and offers simple customization options for comparison of pathways and flux distributions. Our package enables coherent and reproducible workflows as it can be seamlessly integrated with COBRApy and Escher.The source code can be found at https://github.com/Toepfer-Lab/cobramod/ and can be installed with pip. The documentation including tutorials is available at https://cobramod.readthedocs.io/.}",
     issn = {1367-4803},
     doi = {10.1093/bioinformatics/btac119},
     url = {https://doi.org/10.1093/bioinformatics/btac119},
@@ -99,15 +95,14 @@ for more information.
 Development
 -----------
 
-You can contribute to CobraMod by cloning the repository and installing
-it in developer mode using pip :
+You can contribute to CobraMod by cloning the repository and installing it in
+developer mode and using the `dev` dependency group via pip:
 
-    pip install -e .
+    pip install -e ".[dev]"
 
-A conda environment file is supplied (*environment.yml*). This file
-contains all the dependencies to ensure reproducibility of the package.
-We encourage pull requests. CobraMod uses unit testing and new tests are
-welcome.
+Optionally, a conda environment file is supplied (*environment.yml*). This
+file contains all the dependencies to ensure reproducibility of the package. We
+encourage pull requests!
 
 To report bugs and suggestions, please create an issue using the
 corresponding tags at <https://github.com/Toepfer-Lab/cobramod/issues>.
diff --git a/docs/make.bat b/docs/make.bat