Merge pull request #222 from medema-group/chore/github-deploy

Chore/GitHub deploy

.github/workflows/update-version.yml

@@ -0,0 +1,27 @@
+# from https://github.com/actinia-org/actinia-core/blob/main/.github/workflows/update-version.yml
+name: Update Version Number
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  update-version-number:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+      - name: Update Version Number
+        run: |
+          OLD_VERSION=$(grep ^version pyproject.toml | cut -d '"' -f 2)
+          OLD_VERSION="\"$OLD_VERSION\""
+          NEW_VERSION="\"$GITHUB_REF_NAME\""
+          sed -i "s+version = $OLD_VERSION+version = $NEW_VERSION+g" pyproject.toml
+      - name: Commit Changes
+        run: |
+          git config user.name "$GITHUB_ACTOR"
+          git config user.email "[email protected]"
+          git commit -a -m "Update version number to new_version"
+          git push origin HEAD:main

.pre-commit-config.yaml

@@ -19,8 +19,8 @@ repos:
     rev: 6.0.0
     hooks:
       - id: flake8
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
-    hooks:
-      - id: mypy
-        additional_dependencies: [types-PyYAML, types-setuptools]
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.0.1
+  #   hooks:
+  #     - id: mypy
+  #       additional_dependencies: [types-PyYAML, types-setuptools]

big_scape/__main__.py

@@ -9,12 +9,14 @@
 from big_scape.cli import query_cli as query
 from big_scape.cli import benchmark_cli as benchmark
 from big_scape.cli.cli_config import CommandOrder
+from big_scape.utility.version import get_bigscape_version
 
 
 def print_version(ctx, param, value):
     if not value or ctx.resilient_parsing:
         return
-    click.echo("BiG-SCAPE 2.0 beta")
+    bigscape_version = get_bigscape_version()
+    click.echo(f"BiG-SCAPE {bigscape_version}")
     ctx.exit()
 
 

big_scape/run_bigscape.py

@@ -29,6 +29,7 @@
 import big_scape.file_input as bs_files
 
 # import big_scape.genbank as bs_gbk
+from big_scape.utility.version import get_bigscape_version
 import big_scape.data as bs_data
 import big_scape.enums as bs_enums
 import big_scape.comparison as bs_comparison
@@ -45,9 +46,14 @@ def run_bigscape(run: dict) -> None:
     command line arguments, loads the data, runs the analysis and saves the output.
     """
     # starting information
-    # TODO: add automatic updating of version number
+    # this is, lightly and delicately put, *not a great way to get the version*
+    # but after some research, it seems no one had the idea to make this easy
+
+    bigscape_version = get_bigscape_version()
+
     logging.info(
-        "Starting BiG-SCAPE 2.0.0 %s run on %s level with %s alignment and %s weights",
+        "Starting BiG-SCAPE %s %s run on %s level with %s alignment and %s weights",
+        bigscape_version,
         run["mode"],
         run["record_type"].value,
         run["alignment_mode"].value,

big_scape/utility/version.py

@@ -0,0 +1,30 @@
+"""Module that contains helper functions specifically related to the bigscape version
+"""
+
+import toml
+
+from importlib import metadata
+from pathlib import Path
+
+
+def get_bigscape_version() -> str:
+    """Get the version of BiG-SCAPE.
+    The way we retrieve the version is different depending on whether the package is
+    installed or not.
+
+    We need a dedicated library for this because the python community has not figured
+    out that version numbers are pretty core to software development and there is no
+    single place to put them. We want it to only be in the pyproject.toml file and not
+    anywhere else, but this file is not available when installed as a package
+    """
+    # can we get to the pyproject.toml file?
+    print(__file__)
+    pyproject_toml = Path(__file__).parent.parent.parent / "pyproject.toml"
+
+    if pyproject_toml.exists():
+        return toml.load(pyproject_toml)["project"]["version"]
+
+    # if not, we're probably running as a package. get the version of the currently
+    # installed big-scape package
+
+    return metadata.version("big-scape")

environment.yml

@@ -21,3 +21,4 @@ dependencies:
   - pip:
     - click==8.1.7
     - PyYAML==6.0.1
+    - importlib-metadata==8.5.0