diff --git a/.gitignore b/.gitignore
index 3a1ec4c01c7de14864c8405f0cf60cef6a8116ba..bdecffe1d54acd670993aeb7b5d36424f03f797e 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 b70ecaf92cd7962f8a0386c1669495facadf6b0e..c7020b02cfe561ff9ee66bb67806687d8a188399 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/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..00e5c865b272e6d5426b2f2c1622a3623f00cab8
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,65 @@
+# 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-merge-conflict
+ - id: check-toml
+ - id: debug-statements
+ - id: end-of-file-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: 23.3.0
+ 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: 6.3.0
+ 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: v0.13
+ 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
+ args: [
+ --report-level=WARNING,
+ ]
diff --git a/README.rst b/README.rst
index 491a64aec85a13fd9c6a577a42c8c63069df1397..05ddf0fda53a6afa019455917b21432cab0fb171 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``
@@ -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
@@ -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.
diff --git a/development.rst b/development.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4d029e42a767aa17d4ddc14a3bf76d3cd3f9d8d9
--- /dev/null
+++ b/development.rst
@@ -0,0 +1,19 @@
+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
diff --git a/install-dev23a.sh b/install-dev23a.sh
index c01e10b7078becf1735c680f3e5ac8b219910416..5a97c1a1844441efddb3ad560ce89dd3a8fdc2d9 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/pyproject.toml b/pyproject.toml
index 43fabe2af26474f3f89816fcbb6aec5ceb31dd79..951bf9263ac72b3ea70c86a06055686cb92e153b 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",
diff --git a/src/mpsd_software_manager/mpsd_software.py b/src/mpsd_software_manager/mpsd_software.py
index b3b4da2add905eba42bae758ebbcac5fa9c4026a..aa896e693c0de95258e7645b43992109be5cd7bc 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 6efde257bc6818fcbc2c87ea2688a19d11731d82..514c8e5fabd8817fe693ed19e2c50d0ca60abc15 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'