From 5be8a71ff75ac76b5d8e0bc320248d570f861ee1 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Fri, 12 Jul 2024 10:21:51 +0200 Subject: [PATCH 1/7] py-connectome-manipulator: update with new PyPI version. --- .../packages/py-connectome-manipulator/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index af6a02f1569bc4..8197a5ae8a21c1 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -11,9 +11,9 @@ class PyConnectomeManipulator(PythonPackage): """Connectome generator tool.""" homepage = "https://github.com/BlueBrain/connectome-manipulator" - git = "https://github.com/BlueBrain/connectome-manipulator.git" + pypi = "connectome-manipulator/connectome_manipulator-1.0.0.tar.gz" - version("0.0.10", tag="connectome-manipulator-v0.0.10") + version("1.0.0", sha256="f77151bc7569f9d18d77dad04cd9fa24c403989ea28a1811566cc49332a785ef") variant( "convert", From 6e287d057f9e5173d98db2c1a5aed919d6a0e0ea Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Mon, 15 Jul 2024 13:20:00 +0200 Subject: [PATCH 2/7] py-connectome-manipulator: fix dependencies in setup.py --- .../dependencies.patch | 44 +++++++++++++++++++ .../py-connectome-manipulator/package.py | 6 +++ 2 files changed, 50 insertions(+) create mode 100644 bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch new file mode 100644 index 00000000000000..931dcdae06e6ce --- /dev/null +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch @@ -0,0 +1,44 @@ +diff --git a/setup.py b/setup.py +index b01db74160e3a30fe28fda59c435bd8d78b2685f..9229b74e1429419c1c4dd8badf3bcec7105dd604 100644 +--- a/setup.py ++++ b/setup.py +@@ -32,19 +32,19 @@ + license="Apache-2", + install_requires=[ + "bluepysnap==3.0.1", +- "numpy==1.24.3", +- "pandas==2.0.2", +- "progressbar==2.5", +- "pyarrow==14.0.1", +- "scipy==1.10.1", +- "scikit-learn==1.5.0", +- "voxcell==3.1.5", +- "tables==3.8.0", # Optional dependency of pandas.DataFrame.to_hdf() +- "distributed==2023.6.0", # Dask +- "dask-mpi==2022.4.0", ++ "numpy>=1.24.3", ++ "pandas>=2.0.2", ++ "progressbar>=2.5", ++ "pyarrow>=14.0.1", ++ "scipy>=1.10.1", ++ "scikit-learn>=1.5.0", ++ "voxcell>=3.1.5", ++ "tables>=3.8.0", # Optional dependency of pandas.DataFrame.to_hdf() ++ "distributed>=2023.6.0", # Dask ++ "dask-mpi>=2022.4.0", + ], + packages=find_packages(), +- python_requires="==3.10.*", ++ python_requires=">=3.10", + extras_require={"docs": ["sphinx", "sphinx-bluebrain-theme"]}, + entry_points={ + "console_scripts": [ +@@ -59,6 +59,8 @@ + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", ++ "Programming Language :: Python :: 3.11", ++ "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Bio-Informatics", + ], diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index 8197a5ae8a21c1..5b4c26f598206e 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -15,6 +15,12 @@ class PyConnectomeManipulator(PythonPackage): version("1.0.0", sha256="f77151bc7569f9d18d77dad04cd9fa24c403989ea28a1811566cc49332a785ef") + # Fixes dependency and Python version requirements + patch( + "dependencies.patch", + when="@1.0.0", + ) + variant( "convert", default=False, From 7a69f9f53d14aed74b421c51ec5340af084b39b2 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Mon, 15 Jul 2024 13:28:54 +0200 Subject: [PATCH 3/7] =?UTF-8?q?=E2=9D=84=EF=B8=8F?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../packages/py-connectome-manipulator/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index 5b4c26f598206e..8fc61be11df97a 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -16,10 +16,7 @@ class PyConnectomeManipulator(PythonPackage): version("1.0.0", sha256="f77151bc7569f9d18d77dad04cd9fa24c403989ea28a1811566cc49332a785ef") # Fixes dependency and Python version requirements - patch( - "dependencies.patch", - when="@1.0.0", - ) + patch("dependencies.patch", when="@1.0.0") variant( "convert", From 58d1120cd1e092bc5c2dff0eba1ac8bd378d80a9 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Tue, 16 Jul 2024 16:25:45 +0200 Subject: [PATCH 4/7] py-connectome-manipulator: alter dependencies --- .../py-connectome-manipulator/package.py | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index 8fc61be11df97a..f46b297c43af8b 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -27,13 +27,13 @@ class PyConnectomeManipulator(PythonPackage): depends_on("parquet-converters@0.8.0:", type="run", when="+convert") depends_on("py-bluepysnap@3.0.1:", type=("build", "run")) - depends_on("py-numpy", type=("build", "run")) - depends_on("py-pandas", type=("build", "run")) - depends_on("py-progressbar", type=("build", "run")) - depends_on("py-scipy", type=("build", "run")) - depends_on("py-scikit-learn", type=("build", "run")) - depends_on("py-voxcell", type=("build", "run")) - depends_on("py-pyarrow+parquet+dataset", type=("build", "run")) - depends_on("py-distributed", type=("build", "run")) - depends_on("py-dask-mpi", type=("build", "run")) - depends_on("py-tables", type=("build", "run")) + depends_on("py-numpy@1.24.3:", type=("build", "run")) + depends_on("py-pandas@2.0.2:", type=("build", "run")) + depends_on("py-progressbar@2.5:", type=("build", "run")) + depends_on("py-scipy@1.10.1:", type=("build", "run")) + depends_on("py-scikit-learn@1.5.0:", type=("build", "run")) + depends_on("py-voxcell@3.1.5:", type=("build", "run")) + depends_on("py-pyarrow+parquet+dataset@14.0.1:", type=("build", "run")) + depends_on("py-distributed@2023.4.1:", type=("build", "run")) + depends_on("py-dask-mpi@2022.4.0:", type=("build", "run")) + depends_on("py-tables@3.8.0:", type=("build", "run")) From dbcecf417103a925b493f52d0659769a91835c45 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Thu, 18 Jul 2024 15:03:24 +0200 Subject: [PATCH 5/7] py-connectome-manipulator: relax more --- .../packages/py-connectome-manipulator/dependencies.patch | 6 +++--- .../packages/py-connectome-manipulator/package.py | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch index 931dcdae06e6ce..2d0a5d2248943e 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch @@ -17,11 +17,11 @@ index b01db74160e3a30fe28fda59c435bd8d78b2685f..9229b74e1429419c1c4dd8badf3bcec7 - "distributed==2023.6.0", # Dask - "dask-mpi==2022.4.0", + "numpy>=1.24.3", -+ "pandas>=2.0.2", ++ "pandas>=1.5.3", + "progressbar>=2.5", -+ "pyarrow>=14.0.1", ++ "pyarrow>=10.0.1", + "scipy>=1.10.1", -+ "scikit-learn>=1.5.0", ++ "scikit-learn>=1.3.2", + "voxcell>=3.1.5", + "tables>=3.8.0", # Optional dependency of pandas.DataFrame.to_hdf() + "distributed>=2023.6.0", # Dask diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index f46b297c43af8b..617365a5ce06ce 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -28,12 +28,12 @@ class PyConnectomeManipulator(PythonPackage): depends_on("py-bluepysnap@3.0.1:", type=("build", "run")) depends_on("py-numpy@1.24.3:", type=("build", "run")) - depends_on("py-pandas@2.0.2:", type=("build", "run")) + depends_on("py-pandas@1.5.3:", type=("build", "run")) depends_on("py-progressbar@2.5:", type=("build", "run")) depends_on("py-scipy@1.10.1:", type=("build", "run")) - depends_on("py-scikit-learn@1.5.0:", type=("build", "run")) + depends_on("py-scikit-learn@1.3.2:", type=("build", "run")) depends_on("py-voxcell@3.1.5:", type=("build", "run")) - depends_on("py-pyarrow+parquet+dataset@14.0.1:", type=("build", "run")) + depends_on("py-pyarrow+parquet+dataset@10.0.1:", type=("build", "run")) depends_on("py-distributed@2023.4.1:", type=("build", "run")) depends_on("py-dask-mpi@2022.4.0:", type=("build", "run")) depends_on("py-tables@3.8.0:", type=("build", "run")) From d8d0c977cb7daf5d222a95318d81d9d3f9ed48f9 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Mon, 22 Jul 2024 13:46:58 +0200 Subject: [PATCH 6/7] py-connectome-manipulator: fix dependencies. --- .../packages/py-connectome-manipulator/dependencies.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch index 2d0a5d2248943e..1120d074f9d93d 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/dependencies.patch @@ -24,7 +24,7 @@ index b01db74160e3a30fe28fda59c435bd8d78b2685f..9229b74e1429419c1c4dd8badf3bcec7 + "scikit-learn>=1.3.2", + "voxcell>=3.1.5", + "tables>=3.8.0", # Optional dependency of pandas.DataFrame.to_hdf() -+ "distributed>=2023.6.0", # Dask ++ "distributed>=2023.4.1", # Dask + "dask-mpi>=2022.4.0", ], packages=find_packages(), From ebc591ed5798d1c1367cd89dacfa30640e74ea03 Mon Sep 17 00:00:00 2001 From: Matthias Wolf Date: Tue, 13 Aug 2024 14:40:10 +0200 Subject: [PATCH 7/7] bump. --- .../packages/py-connectome-manipulator/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py index 617365a5ce06ce..6bb8a666e6a522 100644 --- a/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py +++ b/bluebrain/repo-bluebrain/packages/py-connectome-manipulator/package.py @@ -13,10 +13,7 @@ class PyConnectomeManipulator(PythonPackage): homepage = "https://github.com/BlueBrain/connectome-manipulator" pypi = "connectome-manipulator/connectome_manipulator-1.0.0.tar.gz" - version("1.0.0", sha256="f77151bc7569f9d18d77dad04cd9fa24c403989ea28a1811566cc49332a785ef") - - # Fixes dependency and Python version requirements - patch("dependencies.patch", when="@1.0.0") + version("1.0.1", sha256="6908e8a19681da9beda577d4f9e6f0fa518060f2a66b76a1ca0027b30478ac40") # FIXME variant( "convert",