[MAINT] convert several maintenance scripts to python (#1268)

* use python instead of bash

* ref

* use python instead of bash

* update make file

Dockerfile

@@ -1,5 +1,12 @@
 FROM bids/base_validator:1.13.1
 
+LABEL org.opencontainers.image.source="https://github.com/cpp-lln-lab/bidspm"
+LABEL org.opencontainers.image.url="https://github.com/cpp-lln-lab/bidspm"
+LABEL org.opencontainers.image.documentation="https://bidspm.readthedocs.io/en/latest"
+LABEL org.opencontainers.image.licenses="GPL-3.0"
+LABEL org.opencontainers.image.title="bidspm"
+LABEL org.opencontainers.image.description="an SPM-centric BIDS app"
+
 ARG DEBIAN_FRONTEND="noninteractive"
 
 ## basic OS tools install octave

Makefile

@@ -59,13 +59,15 @@ update: ## Tries to get the latest version of the current branch from upstream
 fix_submodule: ## Fix any submodules that would not be checked out
 	git submodule update --init --recursive && git submodule update --recursive
 
-bump_version:
-	bash tools/bump_version.sh
+prepare_release:
+	python tools/citation_cff_maint.py
+	python tools/tools/add_links_to_changelog.py
+	python tools/bump_version.py
 
 validate_cff: ## Validate the citation file
 	cffconvert --validate
 
-release: validate_cff bump_version lint manual
+release: validate_cff prepare_release lint manual
 
 
 ################################################################################

README.md

@@ -169,7 +169,7 @@ Please see our [documentation](https://bidspm.readthedocs.io/en/latest/index.htm
   license = {GPL-3.0},
   title = {{bidspm}},
   url = {https://github.com/cpp-lln-lab/bidspm},
-  version = {3.1.0}
+  version = {3.1.0dev}
 }
 ```
 

docs/Makefile

@@ -46,7 +46,7 @@ update_faq:
 	cd faq/spm && faqtory build
 	cd faq/stats && faqtory build
 
-bidspm-manual.pdf:
+bidspm-manual.pdf: update_faq
 	bash create_manual.sh
 
 boilerplate:

src/reports/bidspm.bib

@@ -3,7 +3,7 @@ @software{bidspm
   license   = {GPL-3.0},
   title     = {bidspm},
   url       = {https://github.com/cpp-lln-lab/bidspm},
-  version   = {3.1.0}
+  version   = {3.1.0dev}
   doi       = {10.5281/zenodo.3554331},
   publisher = {Zenodo},
   journal   = {Software}

tools/add_links_to_changlog.py → tools/add_links_to_changelog.py

@@ -2,9 +2,10 @@
 from __future__ import annotations
 
 import re
-from pathlib import Path
 
-change_log = Path(__file__).parent.parent / "CHANGELOG.md"
+from utils import root_dir
+
+change_log = root_dir() / "CHANGELOG.md"
 
 with open(change_log) as f:
     lines = f.readlines()

tools/bump_version.py

@@ -0,0 +1,58 @@
+import re
+import subprocess
+from pathlib import Path
+
+from update_versions_bug_report import main as update_bug_report
+
+from utils import root_dir
+
+
+def read_version_from_citation() -> str:
+    with open(root_dir() / "CITATION.cff", encoding="utf-8") as file:
+        for line in file:
+            if line.startswith("version:"):
+                version = line.strip().replace("version: ", "v")
+                with open(
+                    root_dir() / "version.txt", "w", encoding="utf-8"
+                ) as version_file:
+                    version_file.write(version)
+                return version[1:]  # Remove the leading 'v'
+
+
+def update_file(file_path, pattern, replacement):
+    file_path = Path(file_path)
+    content = file_path.read_text(encoding="utf-8")
+    new_content = re.sub(pattern, replacement, content)
+    file_path.write_text(new_content, encoding="utf-8")
+
+
+def main():
+    version = read_version_from_citation()
+
+    if not version:
+        print("Version not found in CITATION.cff")
+        return
+
+    update_file("README.md", r"version = {.*}", f"version = {{{version}}}")
+    update_file("README.md", r"__version__ = .*", f"version = {{{version}}}")
+    update_file(
+        "src/reports/bidspm.bib", r"  version   = {.*}", f"  version   = {{{version}}}"
+    )
+
+    tools_dir = Path("tools")
+
+    versions_txt_path = tools_dir / "versions.txt"
+    versions = (
+        subprocess.run(["git", "tag", "--list"], capture_output=True, text=True)
+        .stdout.strip()
+        .split("\n")[::-1]
+    )
+    versions_txt_path.write_text("\n".join(versions), encoding="utf-8")
+
+    update_bug_report()
+
+    print(f"Version updated to {version}")
+
+
+if __name__ == "__main__":
+    main()

tools/citation_cff_maint.py

@@ -0,0 +1,51 @@
+"""Update CITATION.cff file."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+import ruamel.yaml
+
+from utils import root_dir
+
+yaml = ruamel.yaml.YAML()
+yaml.indent(mapping=2, sequence=4, offset=2)
+
+
+def citation_file() -> Path:
+    """Return path to CITATIONS.cff file."""
+    return root_dir() / "CITATION.cff"
+
+
+def read_citation_cff() -> dict[str, Any]:
+    """Read CITATION.cff file."""
+    print(f"Reading file: {citation_file()}")
+    with open(citation_file(), encoding="utf8") as f:
+        citation = yaml.load(f)
+    return citation
+
+
+def write_citation_cff(citation: dict[str, Any]) -> None:
+    """Write CITATION.cff file."""
+    print(f"Writing file: {citation_file()}")
+    with open(citation_file(), "w", encoding="utf8") as f:
+        yaml.dump(citation, f)
+
+
+def sort_authors(authors: list[dict[str, str]]) -> list[dict[str, str]]:
+    """Sort authors by given name."""
+    print(" Sorting authors by given name")
+    authors.sort(key=lambda x: x["given-names"])
+    return authors
+
+
+def main() -> None:
+    """Update names.rst and AUTHORS.rst files."""
+    citation = read_citation_cff()
+    citation["authors"] = sort_authors(citation["authors"])
+    write_citation_cff(citation)
+
+
+if __name__ == "__main__":
+    main()

tools/list_uncalled.py

@@ -0,0 +1,42 @@
+"""Print functions that are called less than twice in the code base."""
+
+from pathlib import Path
+
+from rich import print
+
+from utils import root_dir
+
+
+def find_files_with_extension(directory, extension) -> list[Path]:
+    """Recursively find all files in directory with the given extension."""
+    return list(Path(directory).rglob(f"*{extension}"))
+
+
+def main() -> None:
+    src_folder = root_dir() / "src"
+    files = find_files_with_extension(src_folder, ".m")
+
+    for file in files:
+        function = file.stem
+
+        occurrences = []
+        for other_file in files:
+            with open(other_file, encoding="utf-8") as f:
+                content = f.read()
+                if function in content:
+                    occurrences.append(f"{other_file}:{content.find(function)}")
+
+        nb_lines = len(occurrences)
+
+        if nb_lines < 2:
+            print(
+                "\n---------------------------------------------------------------------"
+            )
+            print(function)
+            print()
+            for line in occurrences:
+                print(line)
+
+
+if __name__ == "__main__":
+    main()

tools/update_versions_bug_report.py

@@ -1,21 +1,17 @@
 from __future__ import annotations
 
-from pathlib import Path
-
 import ruamel.yaml
 
+from utils import root_dir
+
 yaml = ruamel.yaml.YAML()
 yaml.indent(mapping=2, sequence=4, offset=2)
 
 
 def main():
-    bug_report = (
-        Path(__file__)
-        .parent.parent.joinpath(".github", "ISSUE_TEMPLATE", "bug_report.yml")
-        .resolve()
-    )
+    bug_report = (root_dir() / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml").absolute()
 
-    versions_file = Path(__file__).parent.joinpath("versions.txt").resolve()
+    versions_file = (root_dir() / "tools" / "versions.txt").absolute()
 
     with open(bug_report, encoding="utf8") as input_file:
         content = yaml.load(input_file)

tools/utils.py

@@ -0,0 +1,8 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+
+def root_dir() -> Path:
+    """Return path to root directory."""
+    return Path(__file__).parent.parent