From b34029b2f489958cd0d1cf3b6366a773b1ba10af Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:09:05 +0200
Subject: [PATCH 01/16] add basic precommit hook config
---
.pre-commit-config.yaml | 58 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
create mode 100644 .pre-commit-config.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..44af4af
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,58 @@
+# Config based on https://gitlab.com/octopus-code/postopus/-/blob/main/.pre-commit-config.yaml
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.4.0
+ hooks:
+ - id: trailing-whitespace
+ - id: check-ast
+ - id: check-docstring-first
+ - id: check-executables-have-shebangs
+ - id: check-json
+ - id: check-merge-conflict
+ - id: check-xml
+ - id: check-yaml
+ - id: check-toml
+ - id: debug-statements
+ - id: end-of-file-fixer
+ - id: requirements-txt-fixer
+ - id: mixed-line-ending
+ args: ['--fix=auto'] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+# other hooks
+# Ruff:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: v0.0.274
+ hooks:
+ - id: ruff
+ args: [--fix, --exit-non-zero-on-fix]
+
+# Black
+- repo: https://github.com/psf/black
+ rev: 22.12.0
+ hooks:
+ - id: black
+ language_version: python3
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+# rev: v1.9.1
+# hooks:
+# - id: blacken-docs
+# additional_dependencies: [black]
+
+# pydocstyle
+- repo: https://github.com/PyCQA/pydocstyle
+ rev: 6.1.1
+ hooks:
+ - id: pydocstyle
+ name: pydocstyle
+ description: pydocstyle is a static analysis tool for checking compliance with Python docstring conventions.
+ entry: pydocstyle
+ language: python
+ types: [python]
+
+- repo: https://github.com/abravalheri/validate-pyproject
+ rev: v0.10.1
+ hooks:
+ - id: validate-pyproject
--
GitLab
From 692798ec9794ed56ac1d2c74060345524be19692 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:14:08 +0200
Subject: [PATCH 02/16] update versions of hooks
---
.pre-commit-config.yaml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 44af4af..4ed6d7c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -22,14 +22,14 @@ repos:
# Ruff:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
- rev: v0.0.274
+ rev: v0.0.269
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
# Black
- repo: https://github.com/psf/black
- rev: 22.12.0
+ rev: 23.3.0
hooks:
- id: black
language_version: python3
@@ -43,7 +43,7 @@ repos:
# pydocstyle
- repo: https://github.com/PyCQA/pydocstyle
- rev: 6.1.1
+ rev: 6.3.0
hooks:
- id: pydocstyle
name: pydocstyle
--
GitLab
From f5dc121fb8ce08cc8f0799cd4b16d79a972d4c4c Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:21:37 +0200
Subject: [PATCH 03/16] add documentation
---
README.rst | 7 +++++--
development.rst | 18 ++++++++++++++++++
2 files changed, 23 insertions(+), 2 deletions(-)
create mode 100644 development.rst
diff --git a/README.rst b/README.rst
index 491a64a..1211d68 100644
--- a/README.rst
+++ b/README.rst
@@ -165,7 +165,7 @@ The ``mpsd-software-manager`` python package.
- Install via pip or pipx.
Pipx commands are:
-
+
- to install: ``pipx install git+https://gitlab.gwdg.de/mpsd-cs/mpsd-software-manager``
- to update: ``pipx upgrade mpsd-software-manager``
- to uninstall: ``pipx uninstall mpsd-software-manager``
@@ -192,7 +192,7 @@ Working example
There is an
`example <https://github.com/mpsd-computational-science/octopus-with-mpsd-software>`__
compilation that shows the complete compilation cycle (including compilation of
-Octopus) using the ``foss2022a-serial`` toolchain.
+Octopus) using the ``foss2022a-serial`` toolchain.
@@ -249,3 +249,6 @@ Frequently asked questions
to experiment with toolchains etc.
+Development
+-----------
+Developers documentation is available at [development.rst](development.rst).
diff --git a/development.rst b/development.rst
new file mode 100644
index 0000000..59ae675
--- /dev/null
+++ b/development.rst
@@ -0,0 +1,18 @@
+Developers Setup
+================
+This section is for developers wanting to contribute to the project.
+
+Setup pre-commit hooks
+----------------------
+The project uses [pre-commit](https://pre-commit.com/) to run some checks before committing code.
+Install pre-commit by running the following command:
+
+ pip install pre-commit
+To setup the pre-commit hooks, run the following command from the root of the project:
+
+ pre-commit install
+
+Then every time you commit, pre-commit will run all checks defined in `.pre-commit-config.yaml`.
+you can run the pre-commit checks manually by running:
+
+ pre-commit run --all-files
--
GitLab
From 1603ed87851d32077d97133a4f3e2ae27ced82a7 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:24:27 +0200
Subject: [PATCH 04/16] update development file link
---
README.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.rst b/README.rst
index 1211d68..93e2339 100644
--- a/README.rst
+++ b/README.rst
@@ -251,4 +251,4 @@ Frequently asked questions
Development
-----------
-Developers documentation is available at [development.rst](development.rst).
+Developers documentation is available at `development.rst<development.rst>`.
--
GitLab
From 760070da8ecfe73173b6603b573a8b514e03d882 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:26:48 +0200
Subject: [PATCH 05/16] correct reference to development.rst
---
README.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.rst b/README.rst
index 93e2339..670c412 100644
--- a/README.rst
+++ b/README.rst
@@ -251,4 +251,4 @@ Frequently asked questions
Development
-----------
-Developers documentation is available at `development.rst<development.rst>`.
+Developers documentation is available at development.rst :ref: `development.rst`
--
GitLab
From 54109267c0a59badf2faed413a71463bb6a85a0f Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:28:33 +0200
Subject: [PATCH 06/16] remove link to development.rst
---
README.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.rst b/README.rst
index 670c412..08583c9 100644
--- a/README.rst
+++ b/README.rst
@@ -251,4 +251,4 @@ Frequently asked questions
Development
-----------
-Developers documentation is available at development.rst :ref: `development.rst`
+Developers documentation is available at development.rst.
--
GitLab
From 557f2d02f492c93317d3ea941b9d7f479f18445b Mon Sep 17 00:00:00 2001
From: Hans Fangohr <hans.fangohr@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 16:53:23 +0200
Subject: [PATCH 07/16] add pre-commit dev-dependency to pyproject.toml
---
pyproject.toml | 1 +
1 file changed, 1 insertion(+)
diff --git a/pyproject.toml b/pyproject.toml
index 43fabe2..951bf92 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,7 @@ Home = "https://gitlab.gwdg.de/mpsd-cs/mpsd-software-manager/"
[project.optional-dependencies]
dev = [
"black",
+ "pre-commit",
"pytest",
"pytest-mock",
"pytest-cov",
--
GitLab
From 5bf66265e8f5b9cc9d2b9435aec2d18f459028e5 Mon Sep 17 00:00:00 2001
From: Hans Fangohr <hans.fangohr@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 15:00:41 +0000
Subject: [PATCH 08/16] Apply changes from Hanss changes
---
development.rst | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/development.rst b/development.rst
index 59ae675..71e325b 100644
--- a/development.rst
+++ b/development.rst
@@ -4,15 +4,15 @@ This section is for developers wanting to contribute to the project.
Setup pre-commit hooks
----------------------
-The project uses [pre-commit](https://pre-commit.com/) to run some checks before committing code.
-Install pre-commit by running the following command:
+The project uses `pre-commit <https://pre-commit.com/>`__ to run some checks before committing code.
+Install pre-commit by running the following command::
pip install pre-commit
-To setup the pre-commit hooks, run the following command from the root of the project:
+To setup the pre-commit hooks, run the following command from the root of the project::
pre-commit install
Then every time you commit, pre-commit will run all checks defined in `.pre-commit-config.yaml`.
-you can run the pre-commit checks manually by running:
+you can run the pre-commit checks manually by running::
pre-commit run --all-files
--
GitLab
From 9c609105199536332818a49269d30f0103331aee Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 17:01:35 +0200
Subject: [PATCH 09/16] remove unused file checks in precommit
---
.pre-commit-config.yaml | 3 ---
1 file changed, 3 deletions(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4ed6d7c..b3bc7b4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,10 +7,7 @@ repos:
- id: check-ast
- id: check-docstring-first
- id: check-executables-have-shebangs
- - id: check-json
- id: check-merge-conflict
- - id: check-xml
- - id: check-yaml
- id: check-toml
- id: debug-statements
- id: end-of-file-fixer
--
GitLab
From 117d781ffd90a337033ce6e87c5cbd0c46f2fcbf Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Wed, 21 Jun 2023 17:05:47 +0200
Subject: [PATCH 10/16] update codeblock syntax
---
development.rst | 1 +
1 file changed, 1 insertion(+)
diff --git a/development.rst b/development.rst
index 71e325b..4d029e4 100644
--- a/development.rst
+++ b/development.rst
@@ -8,6 +8,7 @@ The project uses `pre-commit <https://pre-commit.com/>`__ to run some checks bef
Install pre-commit by running the following command::
pip install pre-commit
+
To setup the pre-commit hooks, run the following command from the root of the project::
pre-commit install
--
GitLab
From e40619350f8f23a3186d1988525c17643a602b8b Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 10:40:56 +0200
Subject: [PATCH 11/16] remove reaquirements txt check
---
.pre-commit-config.yaml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b3bc7b4..ff1842c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,6 @@ repos:
- id: check-toml
- id: debug-statements
- id: end-of-file-fixer
- - id: requirements-txt-fixer
- id: mixed-line-ending
args: ['--fix=auto'] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
--
GitLab
From cfd060a7c6a8c51dbd623f2e3a64ca7e88ed9c06 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 10:41:05 +0200
Subject: [PATCH 12/16] run precommit on all files
---
.gitignore | 2 +-
.gitlab-ci.yml | 5 ++---
install-dev23a.sh | 6 +++---
src/mpsd_software_manager/mpsd_software.py | 16 ++++++++--------
tests/test_mpsd_software.py | 2 +-
5 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/.gitignore b/.gitignore
index 3a1ec4c..bdecffe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,4 @@ dev-23a/
*.log
dist/
build/
-*.egg-info/
\ No newline at end of file
+*.egg-info/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b70ecaf..c7020b0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -91,11 +91,10 @@ test-bullseye:
image: debian:bullseye-slim
script:
- *prepare_debian
- - pytest -v -l
+ - pytest -v -l
test-bookworm:
stage: test
image: debian:bookworm-slim
script:
- *prepare_debian
- - pytest -v -l
-
+ - pytest -v -l
diff --git a/install-dev23a.sh b/install-dev23a.sh
index c01e10b..5a97c1a 100755
--- a/install-dev23a.sh
+++ b/install-dev23a.sh
@@ -1,21 +1,21 @@
#!/bin/bash
# Script to build all toolchains for this MPSD release ( 23a )
# Run this script inside the cloned folder for eg:
-# mpsddeb@mpsd-hpc-ibm-022:/opt_mpsd/linux-debian11/mpsd-software-environments$ ./install-dev23a.sh
+# mpsddeb@mpsd-hpc-ibm-022:/opt_mpsd/linux-debian11/mpsd-software-environments$ ./install-dev23a.sh
set -e
cd ..
mkdir -p dev-23a
cd dev-23a
# clone repo if it doesn't exist yet
-[ -d 'spack-environments' ] || git clone git@gitlab.gwdg.de:mpsd-cs/spack-environments.git
+[ -d 'spack-environments' ] || git clone git@gitlab.gwdg.de:mpsd-cs/spack-environments.git
pushd spack-environments
git checkout dev-23a
git pull
popd
mkdir -p sandybridge
cd sandybridge
-../spack-environments/spack_setup.sh -b global
+../spack-environments/spack_setup.sh -b global
../spack-environments/spack_setup.sh foss2021a-serial
../spack-environments/spack_setup.sh foss2021a-mpi
../spack-environments/spack_setup.sh foss2021a-cuda-mpi
diff --git a/src/mpsd_software_manager/mpsd_software.py b/src/mpsd_software_manager/mpsd_software.py
index b3b4da2..aa896e6 100755
--- a/src/mpsd_software_manager/mpsd_software.py
+++ b/src/mpsd_software_manager/mpsd_software.py
@@ -35,10 +35,10 @@ Build software as on MPSD HPC.
It follows recipes as used on the MPSD HPC system and the (spack-based)
Octopus buildbot. Compiled software is organised into MPSD software release
versions (such as `dev-23a`) and CPU microarchitecture (such as `sandybridge`).
-
+
Compiled packages and toolchains can be activated and used via `module load` as
on the HPC system.
-
+
Further documentation is available in the README.rst file, online at
https://gitlab.gwdg.de/mpsd-cs/mpsd-software-manager/-/blob/main/README.rst
@@ -56,17 +56,17 @@ Examples:
1. Query what package sets and toolchains are available for installation in
release dev-23a
-
+
$> {sys.argv[0]} available dev-23a
-
+
2. Install foss2022a-serial toolchain from the dev-23a release
-
+
$> {sys.argv[0]} install dev-23a foss2022a-serial
-
+
3. Check what package sets and toolchains are installed from release dev-23a
-
+
$> {sys.argv[0]} status dev-23a
-
+
The `status` command also displays the `module use` command needed to load
the created modules.
diff --git a/tests/test_mpsd_software.py b/tests/test_mpsd_software.py
index 6efde25..514c8e5 100644
--- a/tests/test_mpsd_software.py
+++ b/tests/test_mpsd_software.py
@@ -107,7 +107,7 @@ def test_run_method(tmp_path):
def test_prepare_environment(tmp_path):
"""Simulate running preparation of environment.
-
+
Simulate running ./install-software-environment.py --release dev-23a \
--target-directory /tmp/test_prepare_env
prepare_env is run when cmd is not specified, we can test cmd='prepare'
--
GitLab
From 328fafa896bc7ae53e71859009bf87b7773ba32e Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 10:45:31 +0200
Subject: [PATCH 13/16] update precommit vers
---
.pre-commit-config.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ff1842c..82390e6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -18,7 +18,7 @@ repos:
# Ruff:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
- rev: v0.0.269
+ rev: v0.0.274
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
@@ -49,6 +49,6 @@ repos:
types: [python]
- repo: https://github.com/abravalheri/validate-pyproject
- rev: v0.10.1
+ rev: v0.13
hooks:
- id: validate-pyproject
--
GitLab
From 273dfdcf3647a35c69c6dcce7af41be09df17a77 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 10:47:10 +0200
Subject: [PATCH 14/16] add rstcheck precommit
---
.pre-commit-config.yaml | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 82390e6..0009707 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -52,3 +52,11 @@ repos:
rev: v0.13
hooks:
- id: validate-pyproject
+
+- repo: https://github.com/myint/rstcheck
+ rev: v6.1.1
+ hooks:
+ - id: rstcheck
+ additional_dependencies:
+ - sphinx==4.5.0
+ - sphinx-click==3.1.0
--
GitLab
From 2e23d01312766a5442e0d86e68fefc4741602439 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 11:00:41 +0200
Subject: [PATCH 15/16] reduce verbosity of rstcheck
---
.pre-commit-config.yaml | 3 +++
1 file changed, 3 insertions(+)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0009707..00e5c86 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -60,3 +60,6 @@ repos:
additional_dependencies:
- sphinx==4.5.0
- sphinx-click==3.1.0
+ args: [
+ --report-level=WARNING,
+ ]
--
GitLab
From 490c853be54b7b6523eb864eea3289a352bf0b50 Mon Sep 17 00:00:00 2001
From: iamashwin99 <ashwin-kumar.karnad@mpsd.mpg.de>
Date: Thu, 22 Jun 2023 11:00:45 +0200
Subject: [PATCH 16/16] fix issues mentioned by rstcheck
---
README.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.rst b/README.rst
index 08583c9..05ddf0f 100644
--- a/README.rst
+++ b/README.rst
@@ -183,7 +183,7 @@ Requirements for particular toolchains and package sets
- ``foss*-serial`` should compile with the dependencies outlined above
- ``foss*-mpi`` currently needs linux header files installed (to compile the ``knem`` package)
-- ``foss*-cuda-mpi`` (proably as `*-mpi, needs testing TODO)
+- ``foss*-cuda-mpi`` (proably as `*-mpi, needs testing TODO`)
Working example
--
GitLab