From bb33831f36c3e184e05788d3bab7a3c8d9cb4a30 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 13:56:41 +0100
Subject: [PATCH 01/10] feat: add pybaselines
---
packages/py-pybaselines/package.py | 24 ++++++++++++++++++++++++
spack.yaml | 1 +
2 files changed, 25 insertions(+)
create mode 100644 packages/py-pybaselines/package.py
diff --git a/packages/py-pybaselines/package.py b/packages/py-pybaselines/package.py
new file mode 100644
index 00000000..a35ad896
--- /dev/null
+++ b/packages/py-pybaselines/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyPybaselines(PythonPackage):
+ """pybaselines is a library of algorithms for the baseline correction of experimental data."""
+
+ homepage = "https://github.com/derb12/pybaselines"
+ pypi = "pybaselines/pybaselines-1.1.0.tar.gz"
+
+ maintainers("mloshakov", "dennisdoll")
+
+ version("1.1.0", sha256="1f61ca378459af3983d6ca5813610ca587ac33d5b89e3c03bfb5f692bde61526")
+
+ depends_on("python@3.8:", type=("build", "run"))
+
+ depends_on("py-setuptools", type="build")
+
+ depends_on("py-numpy@1.20:", type=("build", "run"))
+ depends_on("py-scipy@1.5:", type=("build", "run"))
diff --git a/spack.yaml b/spack.yaml
index b99a8270..68b3bf2b 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -46,6 +46,7 @@ spack:
- py-netpyne@1.0.6
- py-neurom@3.2.4
- py-neuror@1.6.4
+ - py-pybaselines@1.1.0
- py-pynn@0.12.3 +mpi
- py-pyunicore@1.1.1
- py-quantities-scidash@0.12.4.3
--
GitLab
From fee45ae0ff7b50323d267a3d55c6e59bb3a88977 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 14:14:33 +0100
Subject: [PATCH 02/10] fix: remove dependency from spack.yaml
---
spack.yaml | 1 -
1 file changed, 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 68b3bf2b..b99a8270 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -46,7 +46,6 @@ spack:
- py-netpyne@1.0.6
- py-neurom@3.2.4
- py-neuror@1.6.4
- - py-pybaselines@1.1.0
- py-pynn@0.12.3 +mpi
- py-pyunicore@1.1.1
- py-quantities-scidash@0.12.4.3
--
GitLab
From e409e354411cd6981921c2f00fbfd85c5d802d72 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 15:13:03 +0100
Subject: [PATCH 03/10] feat: add py-ipyfilechooser
---
packages/py-ipyfilechooser/package.py | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
create mode 100644 packages/py-ipyfilechooser/package.py
diff --git a/packages/py-ipyfilechooser/package.py b/packages/py-ipyfilechooser/package.py
new file mode 100644
index 00000000..5d5cd2a6
--- /dev/null
+++ b/packages/py-ipyfilechooser/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyIpyfilechooser(PythonPackage):
+ """Python file chooser widget for use in Jupyter/IPython in conjunction with ipywidgets """
+
+ homepage = "https://github.com/crahan/ipyfilechooser"
+ pypi = "ipyfilechooser/ipyfilechooser-0.6.0.tar.gz"
+
+ maintainers("DennisDoll", "mloshakov", "acascais")
+
+ #license("MIT", checked_by="DennisDoll")
+
+ version("0.6.0", sha256="41df9e4395a924f8e1b78e2804dbe5066dc3fdc233fb07fecfcdc2a0c9a7d8d3")
+
+ depends_on("python@3:", type=("build", "run"))
+ depends_on("py-ipywidgets", type=("build", "run"))
+
+ depends_on("py-setuptools", type="build")
--
GitLab
From eed7d51802eda75996b8ea578e3fb32c7a37e0e9 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 15:21:47 +0100
Subject: [PATCH 04/10] feat: add py-neuralactivitycubic
---
packages/py-neuralactivitycubic/package.py | 41 ++++++++++++++++++++++
spack.yaml | 1 +
2 files changed, 42 insertions(+)
create mode 100644 packages/py-neuralactivitycubic/package.py
diff --git a/packages/py-neuralactivitycubic/package.py b/packages/py-neuralactivitycubic/package.py
new file mode 100644
index 00000000..e9c7afc3
--- /dev/null
+++ b/packages/py-neuralactivitycubic/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+class PyNeuralactivitycubic(PythonPackage):
+ """Computation of local and signal-close-to-noise calcium activity."""
+
+ homepage = "https://github.com/Indoc-Research/NeuralActivityCubic"
+ pypi = "neuralactivitycubic/neuralactivitycubic-0.0.3.tar.gz"
+
+ maintainers("DennisDoll", "mloshakov", "acascais")
+
+ version("0.0.3", sha256="516e99e44a70d83f526a128e653a63c6b7ae4ffbe362fe7854121999a7c8fecb")
+
+ depends_on("python@3.11", type=("build", "run"))
+ depends_on("py-ipywidgets@8.0.2:8", type=("build", "run"))
+ depends_on("py-ipyfilechooser@0.6.0", type=("build", "run"))
+ depends_on("py-imageio@2.30:2", type=("build", "run"))
+ depends_on("py-imageio-ffmpeg@0.4:0.5", type=("build", "run"))
+ depends_on("py-matplotlib@3.8:3.9", type=("build", "run"))
+ depends_on("py-scipy@1.11.4", type=("build", "run"))
+ depends_on("py-numpy@1.26.2", type=("build", "run"))
+ depends_on("py-pandas@2.2.1", type=("build", "run"))
+ depends_on("py-pybaselines@1.1.0", type=("build", "run"))
+ depends_on("py-roifile@2024.1.10", type=("build", "run"))
+ depends_on("py-shapely@2.0.1", type=("build", "run"))
+ depends_on("py-scikit-image@0.22.0", type=("build", "run"))
+
+ depends_on("py-jupyterlab@4.2.3", type=("run"))
+
+ depends_on("py-setuptools", type="build")
+
+
+ @run_after('install')
+ @on_package_attributes(run_tests=True)
+ def install_test(self):
+ with working_dir('spack-test', create=True):
+ python('-c','import neuralactivitycubic')
diff --git a/spack.yaml b/spack.yaml
index b99a8270..753d14fc 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -44,6 +44,7 @@ spack:
- py-neo@0.13.3
- py-nestml@8.0.0
- py-netpyne@1.0.6
+ - py-neuralactivitycubic@0.0.3
- py-neurom@3.2.4
- py-neuror@1.6.4
- py-pynn@0.12.3 +mpi
--
GitLab
From 3fb961ab1f0818ac6febd90b9b6b05df85dade32 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 15:31:14 +0100
Subject: [PATCH 05/10] feat: add py-roifile
---
packages/py-roifile/package.py | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
create mode 100644 packages/py-roifile/package.py
diff --git a/packages/py-roifile/package.py b/packages/py-roifile/package.py
new file mode 100644
index 00000000..151f5faa
--- /dev/null
+++ b/packages/py-roifile/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+# Backported from spack v0.23.0
+class PyRoifile(PythonPackage):
+ """Roifile is a Python library to read, write, create, and plot ImageJ ROIs"""
+
+ homepage = "https://www.cgohlke.com/"
+ pypi = "roifile/roifile-2024.1.10.tar.gz"
+
+ license("BSD-3-Clause", checked_by="A-N-Other")
+
+ version("2024.1.10", sha256="8bbc05a96c0a291429214cb6829426378e89931d1a7d3ad945aa2fea5765e434")
+
+ variant("all", default=True, description="Enable TIFF support")
+
+ depends_on("python@3.9:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+
+ depends_on("py-numpy", type=("build", "run"))
+
+ depends_on("py-matplotlib", type=("build", "run"), when="+all")
+ depends_on("py-tifffile", type=("build", "run"), when="+all")
\ No newline at end of file
--
GitLab
From eb92e8e1ef8b0e3b80374afe197d8857207b40b1 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 15:32:58 +0100
Subject: [PATCH 06/10] fix: py-roifile license
---
packages/py-roifile/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-roifile/package.py b/packages/py-roifile/package.py
index 151f5faa..2e8caa25 100644
--- a/packages/py-roifile/package.py
+++ b/packages/py-roifile/package.py
@@ -13,7 +13,7 @@ class PyRoifile(PythonPackage):
homepage = "https://www.cgohlke.com/"
pypi = "roifile/roifile-2024.1.10.tar.gz"
- license("BSD-3-Clause", checked_by="A-N-Other")
+ # license("BSD-3-Clause", checked_by="A-N-Other")
version("2024.1.10", sha256="8bbc05a96c0a291429214cb6829426378e89931d1a7d3ad945aa2fea5765e434")
--
GitLab
From 4388493a90fbc85d6d13eb71c975960c6f1dd134 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 27 Nov 2024 15:55:03 +0100
Subject: [PATCH 07/10] fix: maybe fixed python versions
---
packages/py-neuralactivitycubic/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-neuralactivitycubic/package.py b/packages/py-neuralactivitycubic/package.py
index e9c7afc3..088c1408 100644
--- a/packages/py-neuralactivitycubic/package.py
+++ b/packages/py-neuralactivitycubic/package.py
@@ -15,7 +15,7 @@ class PyNeuralactivitycubic(PythonPackage):
version("0.0.3", sha256="516e99e44a70d83f526a128e653a63c6b7ae4ffbe362fe7854121999a7c8fecb")
- depends_on("python@3.11", type=("build", "run"))
+ depends_on("python@3.8:", type=("build", "run"))
depends_on("py-ipywidgets@8.0.2:8", type=("build", "run"))
depends_on("py-ipyfilechooser@0.6.0", type=("build", "run"))
depends_on("py-imageio@2.30:2", type=("build", "run"))
--
GitLab
From a60cc146735bda028bc30aa2717d16a774f3ca98 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Thu, 28 Nov 2024 14:49:35 +0100
Subject: [PATCH 08/10] fix python versions one more time
---
create_JupyterLab_kernel.sh | 0
packages/py-roifile/package.py | 2 +-
2 files changed, 1 insertion(+), 1 deletion(-)
mode change 100644 => 100755 create_JupyterLab_kernel.sh
diff --git a/create_JupyterLab_kernel.sh b/create_JupyterLab_kernel.sh
old mode 100644
new mode 100755
diff --git a/packages/py-roifile/package.py b/packages/py-roifile/package.py
index 2e8caa25..1132b381 100644
--- a/packages/py-roifile/package.py
+++ b/packages/py-roifile/package.py
@@ -19,7 +19,7 @@ class PyRoifile(PythonPackage):
variant("all", default=True, description="Enable TIFF support")
- depends_on("python@3.9:", type=("build", "run"))
+ depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
--
GitLab
From aeef7a9f66e5c62e37d4dfa82c669a04e29ca1f4 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Thu, 28 Nov 2024 16:36:17 +0100
Subject: [PATCH 09/10] fix the permission change
---
create_JupyterLab_kernel.sh | 0
1 file changed, 0 insertions(+), 0 deletions(-)
mode change 100755 => 100644 create_JupyterLab_kernel.sh
diff --git a/create_JupyterLab_kernel.sh b/create_JupyterLab_kernel.sh
old mode 100755
new mode 100644
--
GitLab
From 6dfd72b2f3f4a0a39aabb1623f93db86fcf6fd50 Mon Sep 17 00:00:00 2001
From: Matvey Loshakov <mloshakov@indocresearch.org>
Date: Wed, 19 Mar 2025 18:19:03 +0100
Subject: [PATCH 10/10] Updated dependencies for na3
---
packages/py-neuralactivitycubic/package.py | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/packages/py-neuralactivitycubic/package.py b/packages/py-neuralactivitycubic/package.py
index 088c1408..95c94c84 100644
--- a/packages/py-neuralactivitycubic/package.py
+++ b/packages/py-neuralactivitycubic/package.py
@@ -21,15 +21,15 @@ class PyNeuralactivitycubic(PythonPackage):
depends_on("py-imageio@2.30:2", type=("build", "run"))
depends_on("py-imageio-ffmpeg@0.4:0.5", type=("build", "run"))
depends_on("py-matplotlib@3.8:3.9", type=("build", "run"))
- depends_on("py-scipy@1.11.4", type=("build", "run"))
- depends_on("py-numpy@1.26.2", type=("build", "run"))
- depends_on("py-pandas@2.2.1", type=("build", "run"))
- depends_on("py-pybaselines@1.1.0", type=("build", "run"))
- depends_on("py-roifile@2024.1.10", type=("build", "run"))
- depends_on("py-shapely@2.0.1", type=("build", "run"))
- depends_on("py-scikit-image@0.22.0", type=("build", "run"))
-
- depends_on("py-jupyterlab@4.2.3", type=("run"))
+ depends_on("py-scipy@1.11.4:", type=("build", "run"))
+ depends_on("py-numpy@1.26.0:1.9", type=("build", "run"))
+ depends_on("py-pandas@2.2.0:2.4", type=("build", "run"))
+ depends_on("py-pybaselines@1.1.0:", type=("build", "run"))
+ depends_on("py-roifile@2024.1.10:", type=("build", "run"))
+ depends_on("py-shapely@2.0.1:", type=("build", "run"))
+ depends_on("py-scikit-image@0.22.0:", type=("build", "run"))
+
+ depends_on("py-jupyterlab@4.3.3:5", type=("run"))
depends_on("py-setuptools", type="build")
--
GitLab