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bugbear + "BLE", # Flake8-blind-except - flags bare excepts + "C4", # Flake8-comprehensions - best practices in comprehensions "C90", # McCabe - code complexity metric for functions - "N", # PEP8 Naming + "COM", # Flake8-commas - trailing/comma issues "D", # Pydocstyle - docstring formatting + "DOC", # Pydoclint - docstring linting and consistency + "E", # Pycodestyle errors + "EM", # Flake8-errmsg - error message style + "F", # pyflakes + "FAST", # FastAPI - FastAPI-specific linting rules + "FBT", # Flake8-boolean-trap - potential pitfalls with booleans + "FURB", # Refurb - rules for code refurbishment + "G", # Flake8-logging-format - logging format string issues + "I", # isort - import ordering + "ICN", # Flake8-import-conventions - enforces conventional import aliases + "LOG", # Flake8-logging - proper logging usage + "N", # PEP8 Naming + "NPY", # NumPy-specific rules - ensures NumPy coding standards + "PD", # Pandas-vet - checks pandas-specific code practices + "PERF", # Perflint - performance-related checks + "PL", # Pylint rules + "PT", # Flake8-pytest-style - pytest best practices + "Q", # Flake8-quotes - enforces quote style consistency + "RUF", # Ruff-specific rules - additional Ruff checks + "S", # Flake8-bandit - security issues + "SIM", # Flake8-simplify - code simplification hints "UP", # Pyupgrade - upgraded syntax to newer Python versions - "S", # Flake8-bandit – security issues - "BLE", # Flake8-blind-except – flags bare excepts - "FBT", # Flake8-boolean-trap – potential pitfalls with booleans - "A", # Flake8-builtins – misuse of Python built-in names - "COM", # Flake8-commas – trailing/comma issues - "C4", # Flake8-comprehensions – best practices in comprehensions - "EM", # Flake8-errmsg – error message style - "ICN", # Flake8-import-conventions – enforces conventional import aliases - "LOG", # Flake8-logging – proper logging usage - "G", # Flake8-logging-format – logging format string issues - "PT", # Flake8-pytest-style – pytest best practices - "Q", # Flake8-quotes – enforces quote style consistency - "SIM", # Flake8-simplify – code simplification hints - "PD", # Pandas-vet – checks pandas-specific code practices - "NPY", # NumPy-specific rules – ensures NumPy coding standards - "FAST", # FastAPI – FastAPI-specific linting rules - "PERF", # Perflint – performance-related checks - "FURB", # Refurb – rules for code refurbishment - "DOC", # Pydoclint – docstring linting and consistency - "RUF", # Ruff-specific rules – additional Ruff checks + "W", # Pycodestyle warnings ] ignore = [ "COM812", # Redundant with ruff formatter. See: https://docs.astral.sh/ruff/rules/missing-trailing-comma/ From b8531b0f132f7de5f75666727095cee6958178c3 Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 13 Feb 2026 08:38:45 +0100 Subject: [PATCH 3/6] Add Pylint rules Close #83 --- ruff.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ruff.toml b/ruff.toml index ba06c0c..e4ff106 100644 --- a/ruff.toml +++ b/ruff.toml @@ -30,7 +30,7 @@ extend-select = [ "NPY", # NumPy-specific rules - ensures NumPy coding standards "PD", # Pandas-vet - checks pandas-specific code practices "PERF", # Perflint - performance-related checks - "PL", # Pylint rules + "PL", # Pylint rules "PT", # Flake8-pytest-style - pytest best practices "Q", # Flake8-quotes - enforces quote style consistency "RUF", # Ruff-specific rules - additional Ruff checks From 2ee4c70d4f895549e9658736889c8ff1b94730ac Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 13 Feb 2026 08:48:02 +0100 Subject: [PATCH 4/6] chore: Disable Pylint recommandations --- ruff.toml | 7 ++++--- src/mdverse_scrapers/scrapers/mddb.py | 12 ++++++++++-- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/ruff.toml b/ruff.toml index e4ff106..37c177b 100644 --- a/ruff.toml +++ b/ruff.toml @@ -41,7 +41,8 @@ extend-select = [ ] ignore = [ "COM812", # Redundant with ruff formatter. See: https://docs.astral.sh/ruff/rules/missing-trailing-comma/ - "G004", # f-strings are allowed with the loguru module. See https://docs.astral.sh/ruff/rules/logging-f-string/ + "G004", # f-strings are allowed with the loguru module. See https://docs.astral.sh/ruff/rules/logging-f-string/ + "PLR", # No Pylint recommendations ] # Force numpy-style for docstrings @@ -54,6 +55,6 @@ convention = "numpy" "tests/**/*.py" = [ # at least this three should be fine in tests: "S101", # asserts allowed in tests... - "ARG", # Unused function args -> fixtures nevertheless are functionally relevant... - "FBT", # Don't care about booleans as positional arguments in tests, e.g. via @pytest.mark.parametrize() + "ARG", # Unused function args -> fixtures nevertheless are functionally relevant... + "FBT", # Don't care about booleans as positional arguments in tests, e.g. via @pytest.mark.parametrize() ] diff --git a/src/mdverse_scrapers/scrapers/mddb.py b/src/mdverse_scrapers/scrapers/mddb.py index cac1ba0..7c011b8 100644 --- a/src/mdverse_scrapers/scrapers/mddb.py +++ b/src/mdverse_scrapers/scrapers/mddb.py @@ -53,6 +53,7 @@ "base_url": "https://cineca.mddbr.eu", }, } +MAX_NUMBER_OF_DATASETS_IN_DEBUG = 100 def scrape_all_datasets( @@ -140,8 +141,15 @@ def scrape_all_datasets( logger.debug("First dataset metadata on this page:") logger.debug(datasets[0] if datasets else "No datasets on this page") - if scraper and scraper.is_in_debug_mode and len(all_datasets) >= 100: - logger.warning("Debug mode is ON: stopping after 100 datasets.") + if ( + scraper + and scraper.is_in_debug_mode + and len(all_datasets) >= MAX_NUMBER_OF_DATASETS_IN_DEBUG + ): + logger.warning( + "Debug mode is ON: " + f"stopping after {MAX_NUMBER_OF_DATASETS_IN_DEBUG} datasets." + ) return all_datasets logger.success(f"Scraped {len(all_datasets):,} datasets in MDposit.") From 3c7701c3b493d03a10b8e6f759ca3c4c5e53b319 Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 13 Feb 2026 08:52:24 +0100 Subject: [PATCH 5/6] chore: Add typos in pre-commit / prek hooks Fix #84 --- .pre-commit-config.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a5bd615..e8edc8b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -34,7 +34,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Linter and formatter for Python code. - rev: v0.14.14 + rev: v0.15.1 hooks: # Run the linter. # Automatically fix issues where possible. @@ -51,3 +51,9 @@ repos: hooks: - id: bandit args: ["--exclude", "tests"] + +- repo: https://github.com/crate-ci/typos + # Source code spell checker + rev: v1.43.4 + hooks: + - id: typos From c33380011f355d6a2abf1289aca2dcdae1a080b5 Mon Sep 17 00:00:00 2001 From: Pierre Poulain Date: Fri, 13 Feb 2026 09:19:19 +0100 Subject: [PATCH 6/6] chore: Add pre-commit prek hooks for YAML, Markdown and Bash scripts --- .markdownlint.yaml | 10 ++++ .pre-commit-config.yaml | 130 ++++++++++++++++++++++++---------------- README.md | 16 ++--- docs/mddb.md | 14 +++-- 4 files changed, 106 insertions(+), 64 deletions(-) create mode 100644 .markdownlint.yaml diff --git a/.markdownlint.yaml b/.markdownlint.yaml new file mode 100644 index 0000000..6d0364e --- /dev/null +++ b/.markdownlint.yaml @@ -0,0 +1,10 @@ +--- +# Example file: +# https://github.com/DavidAnson/markdownlint/blob/main/schema/.markdownlint.yaml +# MD013/line-length : Line length +# https://github.com/DavidAnson/markdownlint/blob/v0.40.0/doc/md013.md +MD013: + # Number of characters + line_length: 200 + # Exclude citations + blockquotes: false diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e8edc8b..d978d2f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,3 +1,4 @@ +--- # Install pre-commit hooks with: # uv run prek install # Update hooks: @@ -5,55 +6,80 @@ exclude: "scripts/*|tmp/*" repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - # Out-of-the-box hooks for pre-commit. - rev: v6.0.0 - hooks: - # Makes sure files end in a newline and only a newline. - - id: end-of-file-fixer - # Replaces or checks mixed line ending. - - id: mixed-line-ending - # Trims trailing whitespace. - - id: trailing-whitespace - # Attempts to load all json files to verify syntax. - - id: check-json - # Attempts to load all yaml files to verify syntax. - - id: check-yaml - # Attempts to load all TOML files to verify syntax. - - id: check-toml - # Prevent giant files from being committed. - - id: check-added-large-files - # Set max file size to 500 KB. - args: ["--maxkb=500"] - -- repo: https://github.com/asottile/pyupgrade - # Automatically upgrade syntax for newer versions of the Python language. - rev: v3.21.2 - hooks: - - id: pyupgrade - -- repo: https://github.com/astral-sh/ruff-pre-commit - # Linter and formatter for Python code. - rev: v0.15.1 - hooks: - # Run the linter. - # Automatically fix issues where possible. - - id: ruff-check - types: [python] - args: [ --fix ] - # Run the formatter. - - id: ruff-format - types: [python] - -- repo: https://github.com/PyCQA/bandit - # Security linter for Python code. - rev: 1.9.3 - hooks: - - id: bandit - args: ["--exclude", "tests"] - -- repo: https://github.com/crate-ci/typos - # Source code spell checker - rev: v1.43.4 - hooks: - - id: typos + - repo: https://github.com/pre-commit/pre-commit-hooks + # Out-of-the-box hooks for pre-commit. + rev: v6.0.0 + hooks: + # Makes sure files end in a newline and only a newline. + - id: end-of-file-fixer + # Replaces or checks mixed line ending. + - id: mixed-line-ending + # Trims trailing whitespace. + - id: trailing-whitespace + # Attempts to load all json files to verify syntax. + - id: check-json + # Attempts to load all yaml files to verify syntax. + - id: check-yaml + # Attempts to load all TOML files to verify syntax. + - id: check-toml + # Prevent giant files from being committed. + - id: check-added-large-files + # Set max file size to 500 KB. + args: ["--maxkb=500"] + + - repo: https://github.com/asottile/pyupgrade + # Automatically upgrade syntax for newer versions of the Python language. + rev: v3.21.2 + hooks: + - id: pyupgrade + + - repo: https://github.com/astral-sh/ruff-pre-commit + # Linter and formatter for Python code. + rev: v0.15.1 + hooks: + # Run the linter. + # Automatically fix issues where possible. + - id: ruff-check + types: [python] + args: [--fix] + # Run the formatter. + - id: ruff-format + types: [python] + + - repo: https://github.com/PyCQA/bandit + # Security linter for Python code. + rev: 1.9.3 + hooks: + - id: bandit + args: ["--exclude", "tests"] + + - repo: https://github.com/crate-ci/typos + # Source code spell checker + rev: v1.43.4 + hooks: + - id: typos + + - repo: https://github.com/owenlamont/uv-secure + # Scan your uv.lock file for dependencies with known vulnerabilities + rev: 0.15.4 + hooks: + - id: uv-secure + + # YAML + - repo: https://github.com/adrienverge/yamllint + rev: v1.38.0 + hooks: + - id: yamllint + + # Markdown + - repo: https://github.com/igorshubovych/markdownlint-cli + rev: v0.47.0 + hooks: + - id: markdownlint + args: ['--fix'] + + # Shell + - repo: https://github.com/shellcheck-py/shellcheck-py + rev: v0.11.0.1 + hooks: + - id: shellcheck diff --git a/README.md b/README.md index 8bfd1c9..6476a33 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ The scraping takes some time (about 5 hours). A mechanism has been set up to avo Eventually, the scraper will produce two files: `zenodo_datasets.parquet` and `zenodo_files.parquet` :sparkles: -Note that "[false positives](docs/false_positives.md)" have been removed in the scraping proccess. +Note that "[false positives](docs/false_positives.md)" have been removed in the scraping process. ## Scrape Figshare @@ -155,7 +155,7 @@ git clone https://github.com/NMRLipids/BilayerData.git > All metadata are stored in `README.yaml` files under the `Simulations` directory. -2. Extract metadata from simulations +1. Extract metadata from simulations ```bash uv run scripts/scrape_nmrlipids.py \ @@ -212,13 +212,15 @@ uv run scripts/download_files.py --input data/osf_files.tsv \ Option `--withzipfiles` will also get files packaged in zip archives. It means that the script will first download the entire zip archive and then extract the mdp and gro files. -This step will take a couple of hours to complete. Depending on the stability of your internet connection and the availability of the data repository servers, the download might fail for a couple of files. Re-rerun previous commands to resume the download. Files already retrieved will not be downloaded again. +This step will take a couple of hours to complete. +Depending on the stability of your internet connection and the availability of the data repository servers, the download might fail for a couple of files. +Re-rerun previous commands to resume the download. +Files already retrieved will not be downloaded again. Expect about 640 GB of data with the `--withzipfiles` option (~ 8800 gro files and 9500 mdp files) Numbers are indicative only and may vary depend on the time you run this command (databases tend to get bigger and bigger). - ### Parse .mdp files ```bash @@ -231,7 +233,8 @@ This step will take a couple of seconds to run. Results will be saved in `data/g ### Parse .gro files -A rough molecular composition is deduced from the file `params/residue_name.yml` that contains a partial list of residues names organized in categories *protein*, *lipid*, *nucleic*, *glucid* and *water & ion*. +A rough molecular composition is deduced from the file `params/residue_name.yml` +that contains a partial list of residues names organized in categories *protein*, *lipid*, *nucleic*, *glucid* and *water & ion*. ```bash uv run scripts/parse_gro_files.py \ @@ -259,7 +262,6 @@ data/gromacs_gro_files.parquet data/gromacs_mdp_files.parquet ``` - ## Run all script You can run all commands above with the `run_all.sh` script: @@ -271,7 +273,6 @@ bash run_all.sh > [!WARNING] > Be sure, you have have **sufficient** time, bandwidth and disk space to run this command. - ## Upload data on Zenodo (for MDverse mainteners only) *For the owner of the Zenodo record only. Zenodo token requires `deposit:actions` and `deposit:write` scopes.* @@ -283,6 +284,7 @@ uv run scripts/upload_datasets_to_zenodo.py --record 7856524 --metadata params/z ``` Update files: + ```bash uv run scripts/upload_datasets_to_zenodo.py --record 7856524 \ --file data/datasets.parquet \ diff --git a/docs/mddb.md b/docs/mddb.md index 0a040ab..e924ae4 100644 --- a/docs/mddb.md +++ b/docs/mddb.md @@ -1,6 +1,8 @@ # MDDB -> The [MDDB (Molecular Dynamics Data Bank) project](https://mddbr.eu/about/) is an initiative to collect, preserve, and share molecular dynamics (MD) simulation data. As part of this project, **MDposit** is an open platform that provides web access to atomistic MD simulations. Its goal is to facilitate and promote data sharing within the global scientific community to advance research. +> The [MDDB (Molecular Dynamics Data Bank) project](https://mddbr.eu/about/) is an initiative to collect, preserve, and share molecular dynamics (MD) simulation data. +As part of this project, **MDposit** is an open platform that provides web access to atomistic MD simulations. +Its goal is to facilitate and promote data sharing within the global scientific community to advance research. The MDposit infrastructure is distributed across several MDposit nodes. All metadata are accessible through the global node: @@ -29,9 +31,9 @@ A project can contain multiple replicas, each identified by `project_id`.`replic For example, the project [MD-A003ZP](https://mdposit.mddbr.eu/#/id/MD-A003ZP/overview) contains ten replicas: -- `MD-A003ZP.1`: https://mdposit.mddbr.eu/#/id/MD-A003ZP.1/overview -- `MD-A003ZP.2`: https://mdposit.mddbr.eu/#/id/MD-A003ZP.2/overview -- `MD-A003ZP.3`: https://mdposit.mddbr.eu/#/id/MD-A003ZP.3/overview +- `MD-A003ZP.1`: +- `MD-A003ZP.2`: +- `MD-A003ZP.3`: - ... API entrypoint to get all datasets at once: @@ -76,7 +78,9 @@ Title: Description: -> The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol). +> The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. +For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane +(Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol). - [project on MDposit GUI](https://mdposit.mddbr.eu/#/id/MD-A001T1/overview) - [project on MDposit API](https://mdposit.mddbr.eu/api/rest/current/projects/MD-A001T1)