tasks

.test/tasks.py

@@ -0,0 +1,278 @@
+# coding: utf-8
+
+from invoke import task
+from github import Github
+from datetime import datetime
+
+import os.path as op
+import os
+import yaml
+
+
+def get_latest_release(address: str) -> str:
+    git = Github()
+    repo = git.get_repo(address)
+    releases = repo.get_releases()
+    return releases[0].tag_name
+
+
+snakemake_wrappers_version = os.environ.get("SNAKEMAKE_WRAPPERS_VERSION")
+if not snakemake_wrappers_version:
+    print("Searching snakemake wrappers version on the web...")
+    snakemake_wrappers_version = get_latest_release("snakemake/snakemake-wrappers")
+
+fair_genome_indexer_version = os.environ.get("FAIR_GENOME_INDEXER_VERSION")
+if not fair_genome_indexer_version:
+    print("Searching fair-genome-indexer version on the web...")
+    fair_genome_indexer_version = get_latest_release("tdayris/fair_genome_indexer")
+
+
+fair_fastqc_multiqc_version = os.environ.get("FAIR_FASTQC_MULTIQC_VERSION")
+if not fair_fastqc_multiqc_version:
+    print("Searching fair-fastqc-multi-qc version on the web...")
+    fair_fastqc_multiqc_version = get_latest_release("tdayris/fair_fastqc_multiqc")
+
+locations = {
+    "snakefile": "../workflow/Snakefile",
+    "rules": "../workflow/rules/",
+    "scripts": "../workflow/scripts",
+    "envs": "../workflow/envs",
+    "changelog": "../CHANGELOG.md",
+    "cff": "../CITATION.cff",
+}
+for location in locations.values():
+    if not op.exists(location):
+        raise FileNotFoundError(f"Could not find {location=}")
+
+
+def get_future_version(
+    changelog: str = locations["changelog"],
+) -> str:
+    with open(changelog, "r") as changelog_stream:
+        line = next(changelog_stream)
+        version = line.strip("#").strip()
+
+    print(f"Future version is: {version=}")
+    return version
+
+
+future_version = get_future_version()
+
+
+@task
+def clean(
+    c,
+    conda: bool = False,
+    extra: str = "",
+):
+    patterns = [
+        "black.txt",
+        "format.txt",
+        "linter_info.txt",
+        "pipeline.txt",
+        "results",
+        "resources",
+        "report.txt",
+        "report.zip",
+        "resources.md",
+        "resources.tsv",
+        "resources.txt",
+        "summary.tsv",
+        "summary_small.tsv",
+        "docs_update.txt",
+        "logs",
+        "reference",
+        "report",
+        "tmp",
+        "Snakefile",
+        "wrappers_update.txt",
+        "conda_update.txt",
+        "docs_update.txt",
+    ]
+    if conda:
+        patterns.append(".snakemake")
+        patterns.append(".conda")
+
+    for pattern in patterns:
+        if op.exists(pattern):
+            print(f"Removing {pattern=}")
+            c.run(f"rm -rf '{pattern}'")
+        else:
+            print(f"Skipping {pattern=}")
+
+
+@task
+def update_docs_cff(
+    c,
+    to: str = future_version,
+    cff_path: str = locations["cff"],
+):
+    today = datetime.today().strftime("%Y-%m-%d")
+    cff = {
+        "cff-version": "1.2.0",
+        "message": "If you use this software, please cite it as below.",
+        "authors": [
+            {
+                "family-names": "Dayris",
+                "given-names": "Thibault",
+                "orcid": "https://orcid.org/0009-0009-2758-8450",
+            }
+        ],
+        "title": "fair-fastqc-multiqc",
+        "version": future_version,
+        "date-released": today,
+        "url": "https://github.com/tdayris/fair_fastqc_multiqc",
+    }
+    print(cff)
+    with open(cff_path, "w") as yaml_cff_stream:
+        yaml.dump(cff, yaml_cff_stream, default_flow_style=False)
+
+
+@task(update_docs_cff)
+def update_docs_wrappers(c, to: str = snakemake_wrappers_version, future_version: str = future_version):
+    today = datetime.today().strftime("%Y-%m-%d")
+    regex = rf"s|v[0-9]\+\.[0-9]\+\.[0-9]\+/wrappers|{to}/wrappers|g"
+    print(f"Updating snakemake wrappers in README.md to {to=}")
+    c.run(f"sed -i '{regex}' ../README.md >> docs_update.txt 2>&1")
+
+    for root, dirs, files in os.walk("../workflow/report"):
+        for file in files:
+            if file.endswith(".rst"):
+                print(f"Updating snakemake wrappers in '{root}/{file}'...")
+                c.run(f"sed -i '{regex}' '{root}/{file}' >> docs_update.txt 2>&1")
+
+    regex = (
+        's|snakemake_wrappers_prefix: str = "v4.5.0"|'
+        f'snakemake_wrappers_prefix: str = "{to}"|g'
+    )
+    print("Updating '../workflow/rules/common.smk'...")
+    c.run(f"sed -i '{regex}' '../workflow/rules/common.smk' >> update_docs.txt 2>&1")
+
+    regex = (
+        r's|fair-genome-indexer (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
+        f'|fair-genome-indexer (Version {fair_genome_indexer_version})|g;'
+        r's|fair-fastqc-multiqc (Version v\?[0-9]\+\.[0-9]\+\.[0-9]\+)'
+        f'|fair-fastqc-multiqc (Version {future_version})|g'
+
+    )
+    print("Updating '../workflow/report/material_methods.rst'...")
+    c.run(f"sed -i '{regex}' '../workflow/report/material_methods.rst' >> update_docs.txt 2>&1")
+
+    regex = (
+        r's|\:Version\: [0-9]\+\.[0-9]\+\.[0-9]\+ of [0-9]\+\-[0-9]\+\-[0-9]\+$'
+        fr'|\:Version\: {future_version} of {today}|g'
+    )
+    c.run(f"sed -i '{regex}' '../workflow/report/material_methods.rst' >> update_docs.txt 2>&1")
+
+
+
+@task(update_docs_wrappers)
+def update_wrappers_rules(
+    c,
+    to: str = snakemake_wrappers_version,
+    snakefile: str = locations["snakefile"],
+    rules: str = locations["rules"],
+):
+    print(f"Updating {snakefile=}...")
+    c.run(
+        "snakedeploy update-snakemake-wrappers "
+        f"--git-ref '{snakemake_wrappers_version}' '{snakefile}' "
+        ">> wrappers_update.txt 2>&1"
+    )
+
+    for root, dirs, files in os.walk(rules):
+        for file in files:
+            if file == "fair_genome_indexer.smk":
+                c.run(f"""sed -i 's|tag="[0-9]\+\.[0-9]\+\.[0-9]\+"|tag="{fair_genome_indexer_version}"|g' '{root}/{file}' >> wrappers_update.txt 2>&1""")
+            elif file.endswith(".smk"):
+                print(f"Updating '{root}/{file}'...")
+                c.run(
+                    "snakedeploy update-snakemake-wrappers --git-ref "
+                    f"'{snakemake_wrappers_version}' '{root}/{file}' "
+                    ">> wrappers_update.txt 2>&1"
+                )
+            else:
+                print(f"Skipping '{root}/{file}'...")
+
+
+@task(update_wrappers_rules)
+def update_conda(
+    c,
+    envs: str = locations["envs"],
+):
+    for root, dirs, files in os.walk(envs):
+        for file in files:
+            if file.endswith(".yaml"):
+                print(f"Updating '{root}/{file}'. This may take some time...")
+                c.run(
+                    "snakedeploy update-conda-envs --conda-frontend mamba "
+                    f"--pin-envs '{root}/{file}' > conda_update.txt 2>&1"
+                )
+
+
+@task
+def black(c, scripts: str = locations["scripts"]):
+    log: str = "black.txt"
+    for root, dirs, files in os.walk(scripts):
+        for file in files:
+            if file.endswith(".py"):
+                print(f"Formatting '{root}/{file}'...")
+                c.run(f"black '{root}/{file}' >> {log} 2>&1")
+
+
+@task(black)
+def snakefmt(
+    c,
+    snakefile: str = locations["snakefile"],
+    rules: str = locations["rules"],
+):
+    log: str = "format.txt"
+    print(f"Formatting {snakefile=}...")
+    c.run(f"snakefmt '{snakefile}' >> '{log}' 2>&1")
+
+    for root, dirs, files in os.walk(rules):
+        for file in files:
+            if file.endswith(".smk"):
+                print(f"Formatting '{root}/{file}'...")
+                c.run(f"snakefmt '{root}/{file}' >> '{log}' 2>&1")
+
+
+@task(snakefmt)
+def linter(
+    c,
+    snakefile: str = locations["snakefile"],
+):
+    print(f"Linting {snakefile=}...")
+    c.run(f"snakemake --lint -s '{snakefile}' > linter_info.txt 2>&1")
+
+
+@task(linter)
+def pipeline(
+    c,
+    snakefile: str = locations["snakefile"],
+):
+    print("Running pipeline...")
+    cmd = (
+        f"snakemake -s '{snakefile}' "
+        "--cores 7 --restart-times 0 "
+        "--rerun-incomplete --printshellcmds "
+        "--shadow-prefix 'tmp' --rerun-triggers 'mtime' "
+        "--software-deployment-method conda "
+        "--benchmark-extended > pipeline.txt 2>&1"
+    )
+    print(cmd)
+    c.run(cmd)
+
+
+@task(pipeline)
+def report(
+    c,
+    snakefile: str = locations["snakefile"],
+):
+    print("Building test report...")
+    c.run(f"snakemake -s '{snakefile}' --report report.zip > report.txt 2>&1")
+
+@task(clean, update_conda, report)
+def all(c):
+    print("All done.")
+

CITATION.cff

@@ -5,6 +5,6 @@ authors:
 cff-version: 1.2.0
 date-released: '2024-12-04'
 message: If you use this software, please cite it as below.
-title: fair-genome-indexer
-url: https://github.com/tdayris/fair_genome_indexer
+title: fair-fastqc-multiqc
+url: https://github.com/tdayris/fair_fastqc_multiqc
 version: 2.4.2