From 991cd74c5d7d1ccbac25728e017db53799fd4d67 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Wed, 23 Oct 2024 18:16:40 -0500 Subject: [PATCH 1/8] Added pyproject with minimum dependencies --- pyproject.toml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..2561be0 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,11 @@ +[project] +name = "troppo" +version = "0.1.0" +description = "Add your description here" +readme = "README.rst" +requires-python = ">=3.9" +dependencies = [ + "cobamp>=0.2.1", + "cobra>=0.24.0", + "xlrd>=1.2.0" +] From c423b5e3bf1b2e6c53e9eac0230e2195d6f856e7 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:12:43 -0500 Subject: [PATCH 2/8] fix: pyproject for installation setup --- pyproject.toml | 32 +++++++++++++++++++++++++++++--- 1 file changed, 29 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2561be0..1a4fd32 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,11 +1,37 @@ [project] name = "troppo" version = "0.1.0" -description = "Add your description here" +description = "Constraint-based modeling framework for the enumeration of pathway analysis concepts" +authors = [ + {name = "Jorge Ferreira", email = "jorge.ferreira@ceb.uminho.pt"}, + {name = "Vítor Vieira"} +] readme = "README.rst" +license = {file = "LICENSE"} +homepage = "https://github.com/BioSystemsUM/troppo" requires-python = ">=3.9" -dependencies = [ +classifiers = [ + "Development Status :: 4 - Beta", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Intended Audience :: Science/Research", + "Programming Language :: Python :: 3.5", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "'Topic :: Software Development :: Libraries :: Python Modules"' +] + + +[project.urls] +Documentation = "https://github.com/BioSystemsUM/troppo/blob/main/README.rst" + +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[tool.setuptools] +package-dir = { "" = "src" } +packages = { find = "src" } +install_requires = [ "cobamp>=0.2.1", "cobra>=0.24.0", "xlrd>=1.2.0" -] +] \ No newline at end of file From f118f591e0395e1b49537f1371b520e447e44ab5 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:14:14 -0500 Subject: [PATCH 3/8] fix: quotations --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1a4fd32..b70c6ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ classifiers = [ "Intended Audience :: Science/Research", "Programming Language :: Python :: 3.5", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "'Topic :: Software Development :: Libraries :: Python Modules"' + "'Topic :: Software Development :: Libraries :: Python Modules" ] From 9a5dd1af9081abfda2daadd0e5544e4932a70127 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:15:49 -0500 Subject: [PATCH 4/8] fix: project urls --- pyproject.toml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b70c6ef..d0be769 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,6 @@ authors = [ ] readme = "README.rst" license = {file = "LICENSE"} -homepage = "https://github.com/BioSystemsUM/troppo" requires-python = ">=3.9" classifiers = [ "Development Status :: 4 - Beta", @@ -21,7 +20,10 @@ classifiers = [ [project.urls] -Documentation = "https://github.com/BioSystemsUM/troppo/blob/main/README.rst" +Homepage = "https://github.com/BioSystemsUM/troppo" +Documentation = "http://troppo-bisbi.readthedocs.io/" +Repository = "https://github.com/BioSystemsUM/troppo/" +Issues = "https://github.com/BioSystemsUM/troppo/issues" [build-system] requires = ["setuptools>=61.0"] From 7dd6b8b7f07899e4d3a4767624f89d5187dbe129 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:17:32 -0500 Subject: [PATCH 5/8] revert: include dependencies under `project` --- pyproject.toml | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d0be769..e03e1bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,6 +9,11 @@ authors = [ readme = "README.rst" license = {file = "LICENSE"} requires-python = ">=3.9" +dependencies = [ + "cobamp>=0.2.1", + "cobra>=0.24.0", + "xlrd>=1.2.0" +] classifiers = [ "Development Status :: 4 - Beta", "Topic :: Scientific/Engineering :: Bio-Informatics", @@ -26,14 +31,5 @@ Repository = "https://github.com/BioSystemsUM/troppo/" Issues = "https://github.com/BioSystemsUM/troppo/issues" [build-system] -requires = ["setuptools>=61.0"] -build-backend = "setuptools.build_meta" - -[tool.setuptools] -package-dir = { "" = "src" } -packages = { find = "src" } -install_requires = [ - "cobamp>=0.2.1", - "cobra>=0.24.0", - "xlrd>=1.2.0" -] \ No newline at end of file +requires = ["hatchling"] +build-backend = "hatchling.build" From 8fe364c80d39568af2801ef52464b1ab7cdfd5e9 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:18:14 -0500 Subject: [PATCH 6/8] fix: quotations --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e03e1bb..9dc9881 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,10 +17,10 @@ dependencies = [ classifiers = [ "Development Status :: 4 - Beta", "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Software Development :: Libraries :: Python Modules", "Intended Audience :: Science/Research", "Programming Language :: Python :: 3.5", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "'Topic :: Software Development :: Libraries :: Python Modules" + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)" ] From 9b53b71c9ef55de3e11205ded81d4e9de1619074 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:18:32 -0500 Subject: [PATCH 7/8] revert: license location --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9dc9881..dd7ed6a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors = [ {name = "Vítor Vieira"} ] readme = "README.rst" -license = {file = "LICENSE"} +license = {file = "LICENSE.txt"} requires-python = ">=3.9" dependencies = [ "cobamp>=0.2.1", From 3b7302417d32e2fadaee356cc49e8c182a7dd531 Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 25 Oct 2024 12:20:48 -0500 Subject: [PATCH 8/8] Fix description --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dd7ed6a..c55df5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "troppo" version = "0.1.0" -description = "Constraint-based modeling framework for the enumeration of pathway analysis concepts" +description = "Reconstruction algorithms for Python" authors = [ {name = "Jorge Ferreira", email = "jorge.ferreira@ceb.uminho.pt"}, {name = "Vítor Vieira"}