From a26369f2c7fff41be0c0eb736a5bd97ba41d6c65 Mon Sep 17 00:00:00 2001 From: Erik Heeren Date: Wed, 1 Nov 2023 08:46:12 +0100 Subject: [PATCH 1/4] py-bluepyemodel: sync with upstreamed version (dependencies too) --- .../builtin/packages/py-bluepyefe/package.py | 9 ++------- .../packages/py-bluepyemodel/package.py | 10 +++------- .../builtin/packages/py-bluepyopt/package.py | 9 +++------ .../packages/py-currentscape/package.py | 5 +---- .../repos/builtin/packages/py-efel/package.py | 1 - .../builtin/packages/py-morph-tool/package.py | 20 +++++++++---------- .../builtin/packages/py-morphio/package.py | 7 +++---- .../builtin/packages/py-neurom/package.py | 6 +++--- 8 files changed, 25 insertions(+), 42 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-bluepyefe/package.py b/var/spack/repos/builtin/packages/py-bluepyefe/package.py index f14358904be80b..8a15e4edf9e2c5 100644 --- a/var/spack/repos/builtin/packages/py-bluepyefe/package.py +++ b/var/spack/repos/builtin/packages/py-bluepyefe/package.py @@ -1,4 +1,3 @@ -############################################################################## # Copyright 2013-2023 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # @@ -10,21 +9,17 @@ class PyBluepyefe(PythonPackage): """Blue Brain Python E-feature extraction""" homepage = "https://github.com/BlueBrain/BluePyEfe" - pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz" + pypi = "bluepyefe/bluepyefe-2.2.18.tar.gz" git = "https://github.com/BlueBrain/BluePyEfe.git" version("2.2.18", sha256="bfb50c6482433ec2ffb4b65b072d2778bd89ae50d92dd6830969222aabb30275") depends_on("py-setuptools", type="build") - depends_on("py-numpy", type=("build", "run")) + depends_on("py-numpy@:1.23", type=("build", "run")) depends_on("py-neo", type=("build", "run")) depends_on("py-matplotlib", type=("build", "run")) depends_on("py-efel", type=("build", "run")) depends_on("py-scipy", type=("build", "run")) depends_on("py-h5py", type=("build", "run")) depends_on("py-igor", type=("build", "run")) - - def setup_run_environment(self, env): - env.set("NEURON_INIT_MPI", "0") - env.unset("PMI_RANK") diff --git a/var/spack/repos/builtin/packages/py-bluepyemodel/package.py b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py index 89edb5b37f1e5a..f865b9791b622b 100644 --- a/var/spack/repos/builtin/packages/py-bluepyemodel/package.py +++ b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py @@ -10,11 +10,12 @@ class PyBluepyemodel(PythonPackage): """Python library to optimize and evaluate electrical models.""" homepage = "https://github.com/BlueBrain/BluePyEModel" - pypi = "bluepyemodel/bluepyemodel-0.0.57.tar.gz" + pypi = "bluepyemodel/bluepyemodel-0.0.46.tar.gz" - version("0.0.57", sha256="0b91e39e5066ab4a996bd932577b49648169e549c5f05bb3f93e345b4b186093") + version("0.0.46", sha256="ad4c125e491f3337fcc341a4f389b8a616d883ce50fd77d9fb0ea6e13be5da61") depends_on("py-setuptools", type="build") + depends_on("py-setuptools-scm", type="build") depends_on("py-numpy", type=("build", "run")) depends_on("py-scipy", type=("build", "run")) @@ -33,8 +34,3 @@ class PyBluepyemodel(PythonPackage): depends_on("neuron+python@8.0:", type=("build", "run")) depends_on("py-jinja2@3.0.3", when="@0.0.11:", type=("build", "run")) depends_on("py-currentscape@0.0.11:", type=("build", "run")) - - def patch(self): - # This dependency has survived, even though the modules needing it were axed mid - # 2021 - filter_file(r".*psycopg2-binary.*", "", "setup.py") diff --git a/var/spack/repos/builtin/packages/py-bluepyopt/package.py b/var/spack/repos/builtin/packages/py-bluepyopt/package.py index 33028fa8e02dae..ccc39f913558fe 100644 --- a/var/spack/repos/builtin/packages/py-bluepyopt/package.py +++ b/var/spack/repos/builtin/packages/py-bluepyopt/package.py @@ -1,4 +1,3 @@ -############################################################################## # Copyright 2013-2023 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # @@ -18,8 +17,7 @@ class PyBluepyopt(PythonPackage): # patch required to avoid hpe-mpi linked mechanism library patch("pmi_rank.patch") - variant("neuron", default=True, description="Use BluePyOpt together with NEURON") - variant("scoop", default=True, description="Use BluePyOpt together with py-scoop") + variant("scoop", default=False, description="Use BluePyOpt together with py-scoop") depends_on("py-setuptools", type="build") depends_on("py-numpy@1.6:", type=("build", "run")) @@ -30,11 +28,10 @@ class PyBluepyopt(PythonPackage): depends_on("py-pickleshare@0.7.3:", type=("build", "run")) depends_on("py-jinja2@2.8:", type=("build", "run")) depends_on("py-future", type=("build", "run")) - depends_on("py-pebble@4.3.10:", type=("build", "run")) + depends_on("py-pebble@4.6:", type=("build", "run")) depends_on("py-scoop@0.7:", type=("build", "run"), when="+scoop") - depends_on("neuron@7.4:", type=("build", "run"), when="+neuron") + depends_on("neuron@7.4:", type=("build", "run")) def setup_run_environment(self, env): env.unset("PMI_RANK") env.set("NEURON_INIT_MPI", "0") - env.prepend_path("PATH", self.spec["py-ipyparallel"].prefix.bin) diff --git a/var/spack/repos/builtin/packages/py-currentscape/package.py b/var/spack/repos/builtin/packages/py-currentscape/package.py index 27fbb32a33958e..eb6d75be89c8ab 100644 --- a/var/spack/repos/builtin/packages/py-currentscape/package.py +++ b/var/spack/repos/builtin/packages/py-currentscape/package.py @@ -13,10 +13,7 @@ class PyCurrentscape(PythonPackage): git = "https://github.com/BlueBrain/Currentscape.git" pypi = "currentscape/currentscape-1.0.12.tar.gz" - version( - "1.0.12", - sha256="d83c5a58074e4d612553472a487e5d1d2854dc4d5c161817c6bafdf4a5988011", - ) + version("1.0.12", sha256="d83c5a58074e4d612553472a487e5d1d2854dc4d5c161817c6bafdf4a5988011") depends_on("py-setuptools", type=("build", "run")) depends_on("py-setuptools-scm", type=("build",)) diff --git a/var/spack/repos/builtin/packages/py-efel/package.py b/var/spack/repos/builtin/packages/py-efel/package.py index dc696624b045cf..a33749b9af75eb 100644 --- a/var/spack/repos/builtin/packages/py-efel/package.py +++ b/var/spack/repos/builtin/packages/py-efel/package.py @@ -1,4 +1,3 @@ -############################################################################## # Copyright 2013-2023 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # diff --git a/var/spack/repos/builtin/packages/py-morph-tool/package.py b/var/spack/repos/builtin/packages/py-morph-tool/package.py index f0c3752c38a603..7927b468c07edf 100644 --- a/var/spack/repos/builtin/packages/py-morph-tool/package.py +++ b/var/spack/repos/builtin/packages/py-morph-tool/package.py @@ -13,27 +13,27 @@ class PyMorphTool(PythonPackage): git = "https://github.com/BlueBrain/morph-tool.git" pypi = "morph-tool/morph-tool-2.9.1.tar.gz" - version("develop", branch="master") + version("master", branch="master") version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc") version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47") - variant("neuron", default=False, description="Enable additional neuron support") - variant("plotly", default=False, description="Enable additional plotly support") + variant("nrn", default=False, description="Enable additional neuron support") + variant("plot", default=False, description="Enable additional plotly support") variant("parallel", default=False, description="Enable additional parallel support") - depends_on("py-setuptools", type=("build", "run")) - depends_on("py-setuptools-scm", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-setuptools-scm", type="build") depends_on("py-click@6.7:", type=("build", "run")) depends_on("py-deprecation@2.1.0:", type=("build", "run")) depends_on("py-more-itertools@8.6.0:", type=("build", "run")) - depends_on("py-morphio@3,develop", type=("build", "run")) - depends_on("py-neurom@3,develop", type=("build", "run")) + depends_on("py-morphio@3", type=("build", "run")) + depends_on("py-neurom@3", type=("build", "run")) depends_on("py-numpy@1.14:", type=("build", "run")) depends_on("py-pandas@1.0.3:", type=("build", "run")) depends_on("py-xmltodict@0.12.0:", type=("build", "run")) - depends_on("py-plotly@4.1.0:", type=("build", "run"), when="+plotly") + depends_on("py-plotly@4.1.0:", type=("build", "run"), when="+plot") depends_on("py-dask+bag@2.19.0:", type=("build", "run"), when="+parallel") - depends_on("neuron+python@7.8:", type=("build", "run"), when="+neuron") - depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+neuron") + depends_on("neuron+python@7.8:", type=("build", "run"), when="+nrn") + depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+nrn") diff --git a/var/spack/repos/builtin/packages/py-morphio/package.py b/var/spack/repos/builtin/packages/py-morphio/package.py index 802014fa3978ee..a5a9fee7deaf3c 100644 --- a/var/spack/repos/builtin/packages/py-morphio/package.py +++ b/var/spack/repos/builtin/packages/py-morphio/package.py @@ -19,13 +19,12 @@ class PyMorphio(PythonPackage): version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6") - depends_on("py-setuptools", type="build") + depends_on("py-setuptools@24.2:", type="build") depends_on("py-setuptools-scm", type="build") depends_on("ninja", type="build") depends_on("cmake@3.2:", type="build") depends_on("py-numpy@1.14.1:", type=("build", "run")) - if sys.platform == "win32": - depends_on("py-h5py@3", type=("build", "run")) - else: + depends_on("py-h5py@3", when="platform=windows", type=("build", "run")) + if sys.platform != "win32": depends_on("hdf5") diff --git a/var/spack/repos/builtin/packages/py-neurom/package.py b/var/spack/repos/builtin/packages/py-neurom/package.py index 8e7d95e702904b..19bad5fc7b94c7 100644 --- a/var/spack/repos/builtin/packages/py-neurom/package.py +++ b/var/spack/repos/builtin/packages/py-neurom/package.py @@ -13,14 +13,14 @@ class PyNeurom(PythonPackage): git = "https://github.com/BlueBrain/NeuroM.git" pypi = "neurom/neurom-2.2.1.tar.gz" - version("develop", branch="master") + version("master", branch="master") version("3.2.4", sha256="a584e0979b54deee906dd716ea90de20773e20b527d83960d0fe655b0905eb4a") variant("plotly", default=False, description="Enable plotly support") - depends_on("py-setuptools@0.42:", type=("build", "run")) + depends_on("py-setuptools@42:", type=("build", "run")) depends_on("py-setuptools-scm", type="build") - depends_on("py-wheel", type="build") + depends_on("python@3.8:", type=("build", "run")) depends_on("py-click@7.0:", type=("build", "run")) depends_on("py-matplotlib@3.2.1:", type=("build", "run")) From df46a0a0361f628c0d566283744dce8a19633627 Mon Sep 17 00:00:00 2001 From: Erik Heeren Date: Wed, 1 Nov 2023 10:53:02 +0100 Subject: [PATCH 2/4] py-bluepyemodel: newer version is available --- var/spack/repos/builtin/packages/py-bluepyemodel/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-bluepyemodel/package.py b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py index f865b9791b622b..8cac0b128c1a6d 100644 --- a/var/spack/repos/builtin/packages/py-bluepyemodel/package.py +++ b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py @@ -12,6 +12,7 @@ class PyBluepyemodel(PythonPackage): homepage = "https://github.com/BlueBrain/BluePyEModel" pypi = "bluepyemodel/bluepyemodel-0.0.46.tar.gz" + version("0.0.57", sha256="0b91e39e5066ab4a996bd932577b49648169e549c5f05bb3f93e345b4b186093") version("0.0.46", sha256="ad4c125e491f3337fcc341a4f389b8a616d883ce50fd77d9fb0ea6e13be5da61") depends_on("py-setuptools", type="build") From ccf9589073c59907f0a92adbf7533cedf767fe45 Mon Sep 17 00:00:00 2001 From: Erik Heeren Date: Thu, 2 Nov 2023 11:22:04 +0100 Subject: [PATCH 3/4] py-region-grower: py-morph-tool variant is called nrn now --- bluebrain/repo-bluebrain/packages/py-region-grower/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bluebrain/repo-bluebrain/packages/py-region-grower/package.py b/bluebrain/repo-bluebrain/packages/py-region-grower/package.py index e37f215d8af5e0..4a9d15a92c8dd3 100644 --- a/bluebrain/repo-bluebrain/packages/py-region-grower/package.py +++ b/bluebrain/repo-bluebrain/packages/py-region-grower/package.py @@ -24,7 +24,7 @@ class PyRegionGrower(PythonPackage): depends_on("py-dask+dataframe+distributed@2023.3.2:", type=("build", "run")) depends_on("py-diameter-synthesis@0.5.4:", type=("build", "run")) depends_on("py-morphio@3.3.6:3", type=("build", "run")) - depends_on("py-morph-tool@2.9.0:2 +neuron", type=("build", "run")) + depends_on("py-morph-tool@2.9.0:2 +nrn", type=("build", "run")) depends_on("py-neuroc@0.2.8:", type=("build", "run")) depends_on("py-neurom@3.0:3", type=("build", "run")) depends_on("py-neurots@3.4.2:3", type=("build", "run")) From ffda5e7e0aef08961e695bf091877d321f83c321 Mon Sep 17 00:00:00 2001 From: Erik Heeren Date: Mon, 6 Nov 2023 11:08:06 +0100 Subject: [PATCH 4/4] deploy: py-morph-tool variant name has changed --- bluebrain/deployment/environments/applications_nse.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bluebrain/deployment/environments/applications_nse.yaml b/bluebrain/deployment/environments/applications_nse.yaml index 509ebbe5c15ad6..08e7d4f27ac172 100644 --- a/bluebrain/deployment/environments/applications_nse.yaml +++ b/bluebrain/deployment/environments/applications_nse.yaml @@ -57,6 +57,6 @@ spack: - py-minis-validation - py-morphio - py-neuror - - py-morph-tool+neuron + - py-morph-tool+nrn - py-region-grower - py-cwl-registry