# HG changeset patch # User francesco_lapi # Date 1748268398 0 # Node ID fa041ec0b75564479eab0a68e6cec277a7909085 # Parent c9647b137ab669d219453499002c73a6847ffd2b Uploaded diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/.gitignore Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,6 @@ +__pycache__/ +cobraxy.egg-info/ +.venv/ +.vscode/ +outputs/ +build/ \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/cobraxy-0.1.0.tar.gz Binary file COBRAxy/dist/cobraxy-0.1.0.tar.gz has changed diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/cobraxy/meta.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/cobraxy/meta.yaml Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,80 @@ +{% set name = "cobraxy" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: file:///C:/Users/f.lapi/Documents/GitHub/COBRAxy/dist/cobraxy-0.1.0.tar.gz + sha256: 9445b95e62cfe5233c29baabd5c02a7732d3d096cccdd99cfea13948d1509d9e + +build: + entry_points: + - custom_data_generator=custom_data_generator:main + - flux_simulation=flux_simulation:main + - flux_to_map=flux_to_map:main + - marea_cluster=marea_cluster:main + - marea=marea:main + - ras_generator=ras_generator:main + - ras_to_bounds=ras_to_bounds:main + - rps_generator=rps_generator:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.8.20,<3.12 + - pip + - setuptools + run: + - python >=3.8.20,<3.12 + - cairosvg ==2.7.1 + - cobra ==0.29.0 + - joblib ==1.4.2 + - lxml ==5.2.2 + - matplotlib-base ==3.7.3 + - numpy ==1.24.4 + - pandas ==2.0.3 + - pyvips ==2.2.3 # [linux or osx] + - scikit-learn ==1.3.2 + - scipy ==1.10.1 + - seaborn ==0.13.0 + - svglib ==1.5.1 + pip: + - pyvips==2.2.3 # [win] + +test: + imports: + - utils + - custom_data_generator + - flux_simulation + - marea_cluster + - ras_generator + - ras_to_bounds + - rps_generator + commands: + - pip install pyvips==2.2.3 + - python -c "import pyvips; print('pyvips version:', pyvips.__version__)" + - pip check + - custom_data_generator --help + - flux_simulation --help + - flux_to_map --help + - marea_cluster --help + - marea --help + - ras_generator --help + - ras_to_bounds --help + - rps_generator --help + requires: + - pip + +about: + home: https://github.com/CompBtBs/COBRAxy.git + summary: A collection of tools for metabolic flux analysis in Galaxy. + #license: '' + #license_file: PLEASE_ADD_LICENSE_FILE + +extra: + recipe-maintainers: + - Francesco2304 diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/channeldata.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/channeldata.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"channeldata_version":1,"packages":{"cobraxy":{"activate.d":false,"binary_prefix":false,"deactivate.d":false,"home":"https://github.com/CompBtBs/COBRAxy.git","post_link":false,"pre_link":false,"pre_unlink":false,"run_exports":{},"source_url":"file:///C:/Users/f.lapi/Documents/GitHub/COBRAxy/dist/cobraxy-0.1.0.tar.gz","subdirs":["noarch"],"summary":"A collection of tools for metabolic flux analysis in Galaxy.","text_prefix":false,"timestamp":1741366947,"version":"0.1.0"}},"subdirs":["noarch","win-64"]} diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/index.html Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,90 @@ + + + release + + + +

release

+

RSS Feed   channeldata.json

+noarch   win-64    + + + + + + + + + + + + + + + +
PackageLatest VersionDocDevLicensewin-64noarch Summary
cobraxy0.1.0X A collection of tools for metabolic flux analysis in Galaxy.
+
Updated: 2025-03-07 17:03:09 +0000 - Files: 1
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release/noarch

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FilenameSizeLast ModifiedSHA256MD5
repodata.json601 B2025-03-07 17:02:28 +0000f8cfc8b6d1f71e9b13db3152bbe3fdfac3d5ca94c748a279599dd6f6872a5ba221106deab69c56a7e13f5167091e9860
repodata_from_packages.json601 B2025-03-07 17:02:28 +0000f8cfc8b6d1f71e9b13db3152bbe3fdfac3d5ca94c748a279599dd6f6872a5ba221106deab69c56a7e13f5167091e9860
cobraxy-0.1.0-py_0.conda50 KB2025-03-07 17:02:27 +0000caba0a0729ba111c4a65a6c1450653275f6e0cfdeb052f7e7a8981cc2bbc447e3ce06fbcbd3360c12bac9adf7957ab85
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Updated: 2025-03-07 17:03:09 +0000 - Files: 1
+ + \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/noarch/repodata.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/noarch/repodata.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"info":{"subdir":"noarch"},"packages":{},"packages.conda":{"cobraxy-0.1.0-py_0.conda":{"build":"py_0","build_number":0,"depends":["cairosvg 2.7.1","cobra 0.29.0","joblib 1.4.2","lxml 5.2.2","matplotlib-base 3.7.3","numpy 1.24.4","pandas 2.0.3","python >=3.8.20,<3.12","scikit-learn 1.3.2","scipy 1.10.1","seaborn 0.13.0","svglib 1.5.1"],"md5":"3ce06fbcbd3360c12bac9adf7957ab85","name":"cobraxy","noarch":"python","sha256":"caba0a0729ba111c4a65a6c1450653275f6e0cfdeb052f7e7a8981cc2bbc447e","size":51008,"subdir":"noarch","timestamp":1741366947437,"version":"0.1.0"}},"removed":[],"repodata_version":1} \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/noarch/repodata_from_packages.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/noarch/repodata_from_packages.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"info":{"subdir":"noarch"},"packages":{},"packages.conda":{"cobraxy-0.1.0-py_0.conda":{"build":"py_0","build_number":0,"depends":["cairosvg 2.7.1","cobra 0.29.0","joblib 1.4.2","lxml 5.2.2","matplotlib-base 3.7.3","numpy 1.24.4","pandas 2.0.3","python >=3.8.20,<3.12","scikit-learn 1.3.2","scipy 1.10.1","seaborn 0.13.0","svglib 1.5.1"],"md5":"3ce06fbcbd3360c12bac9adf7957ab85","name":"cobraxy","noarch":"python","sha256":"caba0a0729ba111c4a65a6c1450653275f6e0cfdeb052f7e7a8981cc2bbc447e","size":51008,"subdir":"noarch","timestamp":1741366947437,"version":"0.1.0"}},"removed":[],"repodata_version":1} \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/win-64/.cache/cache.db Binary file COBRAxy/dist/release/win-64/.cache/cache.db has changed diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/win-64/current_repodata.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/win-64/current_repodata.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"info":{"subdir":"win-64"},"packages":{},"packages.conda":{},"removed":[],"repodata_version":1} \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/win-64/index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/win-64/index.html Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,70 @@ + + + release/win-64 + + + +

release/win-64

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FilenameSizeLast ModifiedSHA256MD5
repodata.json96 B2025-03-07 16:59:38 +000080f1769e75036891cfc10fc66eca8134a78b12e6e5cae86132db6148cf970bb1fae3e0350ae934ae1572b2b0f28dcf74
repodata_from_packages.json96 B2025-03-07 16:59:38 +000080f1769e75036891cfc10fc66eca8134a78b12e6e5cae86132db6148cf970bb1fae3e0350ae934ae1572b2b0f28dcf74
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Updated: 2025-03-07 17:03:09 +0000 - Files: 0
+ + \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/win-64/repodata.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/win-64/repodata.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"info":{"subdir":"win-64"},"packages":{},"packages.conda":{},"removed":[],"repodata_version":1} \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/dist/release/win-64/repodata_from_packages.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/dist/release/win-64/repodata_from_packages.json Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,1 @@ +{"info":{"subdir":"win-64"},"packages":{},"packages.conda":{},"removed":[],"repodata_version":1} \ No newline at end of file diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/local/svg metabolic maps/ENGRO2_map.svg --- a/COBRAxy/local/svg metabolic maps/ENGRO2_map.svg Thu May 22 16:56:13 2025 +0000 +++ b/COBRAxy/local/svg metabolic maps/ENGRO2_map.svg Mon May 26 14:06:38 2025 +0000 @@ -7,7 +7,7 @@ version="1.1" id="svg1344" sodipodi:docname="ENGRO2_map.svg" - inkscape:version="1.3 (0e150ed6c4, 2023-07-21)" + inkscape:version="1.4 (86a8ad7, 2024-10-11)" xml:space="preserve" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" @@ -137,13 +137,13 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="0.43840621" - inkscape:cx="900.9909" - inkscape:cy="2409.8655" - inkscape:window-width="1920" - inkscape:window-height="1009" - inkscape:window-x="-8" - inkscape:window-y="-8" + inkscape:zoom="2.48" + inkscape:cx="431.85483" + inkscape:cy="2394.9596" + inkscape:window-width="2560" + inkscape:window-height="1494" + inkscape:window-x="-11" + inkscape:window-y="-11" inkscape:window-maximized="1" inkscape:current-layer="Legend body" showgrid="true">Flux-inversion: same direction of the arrow in dataset2, opposite direction in dataset1.Flux-inversion: same direction of the arrow in dataset2, opposite direction in dataset1. + marea_macros.xml diff -r c9647b137ab6 -r fa041ec0b755 COBRAxy/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COBRAxy/setup.py Mon May 26 14:06:38 2025 +0000 @@ -0,0 +1,59 @@ +from setuptools import setup, find_packages + +setup( + name='cobraxy', + version='0.1.0', + description='A collection of tools for metabolic flux analysis in Galaxy.', + long_description=open('README.md').read(), + long_description_content_type='text/markdown', + author='', + author_email='', + url='https://github.com/CompBtBs/COBRAxy.git', + license='', + packages=find_packages(include=["utils", "utils.*"]), + py_modules=[ + 'custom_data_generator', + 'flux_simulation', + 'flux_to_map', + 'marea_cluster', + 'marea', + 'ras_generator', + 'ras_to_bounds', + 'rps_generator' + ], + include_package_data=True, + install_requires=[ + 'cairosvg==2.7.1', + 'cobra==0.29.0', + 'joblib==1.4.2', + 'lxml==5.2.2', + 'matplotlib==3.7.3', + 'numpy==1.24.4', + 'pandas==2.0.3', + 'pyvips==2.2.3', + 'scikit-learn==1.3.2', + 'scipy==1.11', + 'seaborn==0.13.0', + 'svglib==1.5.1', + 'anndata==0.8.0', + 'pydeseq2==0.5.1' + ], + entry_points={ + 'console_scripts': [ + 'custom_data_generator=custom_data_generator:main', + 'flux_simulation=flux_simulation:main', + 'flux_to_map=flux_to_map:main', + 'marea_cluster=marea_cluster:main', + 'marea=marea:main', + 'ras_generator=ras_generator:main', + 'ras_to_bounds=ras_to_bounds:main', + 'rps_generator=rps_generator:main' + ], + }, + classifiers=[ + 'Programming Language :: Python :: 3', + 'License :: OSI Approved :: MIT License', + 'Operating System :: OS Independent', + ], + python_requires='>=3.8.20,<3.12', +)