Merge branch 'master' into feat/lint-repodata-patches

CHANGELOG.md

@@ -1,5 +1,20 @@
 # Changelog
 
+### [2.3.4](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.3...v2.3.4) (2023-07-15)
+
+
+### Bug Fixes
+
+* update pinning for libxml2 due to conda-forge migration ([#903](https://www.github.com/bioconda/bioconda-utils/issues/903)) ([ee226f8](https://www.github.com/bioconda/bioconda-utils/commit/ee226f8e84a0820430c105412f08714a4de34715))
+
+### [2.3.3](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.2...v2.3.3) (2023-07-06)
+
+
+### Bug Fixes
+
+* adds alternate lookup if base lookup fails ([#896](https://www.github.com/bioconda/bioconda-utils/issues/896)) ([17a1475](https://www.github.com/bioconda/bioconda-utils/commit/17a147508a64bdafb6031c05a75724b25669ec8d))
+* update r-base pinning ([#901](https://www.github.com/bioconda/bioconda-utils/issues/901)) ([54d8702](https://www.github.com/bioconda/bioconda-utils/commit/54d870205d823b6f292df5258b980cbbaa97df77))
+
 ### [2.3.2](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.1...v2.3.2) (2023-06-29)
 
 

bioconda_utils/bioconda_utils-conda_build_config.yaml

@@ -30,7 +30,14 @@ bamtools:
 # NOTE: Workaround https://github.com/conda/conda-build/issues/3974 we slightly alter the values
 #       from conda-forge-pinnings here (inserting '.*' or ' ' which should be ignored later on).
 r_base:
-  - "4.2.*"
+  - "4.3.*"
+
+# Note: this is a (hopefully) temporary fix for the r-base 4.3 migration. That package was built 
+# with libxml2 2.11, but that migration on conda-forge isn't yet complete. Consequently conda-forge-pinning
+# still has libxml2 2.10. That means that there are a number of R and Bioconductor packages we can't currently
+# build without manually changing out libxml2 pinning.
+libxml2:
+  - "2.11.*"
 
 python:
   - 3.10.*  *_cpython

bioconda_utils/cli.py

@@ -465,7 +465,7 @@ def build(recipe_folder, config, packages="*", git_range=None, testonly=False,
             logger.warning(f"Using tag {image_tag} for docker image, since there is no image for a not yet release version ({VERSION}).")
         else:
             image_tag = VERSION
-        docker_base_image = f"quay.io/bioconda/bioconda-utils-build-env-cos7:{image_tag}"
+        docker_base_image = docker_base_image or f"quay.io/bioconda/bioconda-utils-build-env-cos7:{image_tag}"
         logger.info(f"Using docker image {docker_base_image} for building.")
 
         docker_builder = docker_utils.RecipeBuilder(

bioconda_utils/hosters.py

@@ -326,7 +326,61 @@ class GithubBase(OrderedHTMLHoster):
 class GithubRelease(GithubBase):
     """Matches release artifacts uploaded to Github"""
     link_pattern = r"/{account}/{project}/releases/download/{tag}/{fname}{ext}?"
+    alt_releases_formats = ["https://api.github.com/repos/{account}/{project}/releases"]
 
+    async def get_versions(self, req, orig_version):
+        # first, try the older version when HTML worked
+        matches = await super().get_versions(req, orig_version)
+        if len(matches) > 0:
+            return matches
+
+        # old version found nothing, try with the alternate github API URLs which return JSON
+        self.releases_urls = [
+            template.format_map(self.vals)
+            for template in self.alt_releases_formats
+        ]
+
+        # this is basically copied from a mixture of the base version and the JSON version
+        # need to compile the link regex
+        exclude = set(self.exclude)
+        vals = {key: val
+                for key, val in self.vals.items()
+                if key not in exclude}
+        link_pattern = replace_named_capture_group(self.link_pattern_compiled, vals)
+        link_re = re.compile(link_pattern)
+
+        # now iterate over the alter release URLs
+        matches = []
+        for url in self.releases_urls:
+            text = await req.get_text_from_url(url)
+            data = json.loads(text)
+
+            # structured as an array of tagged releases
+            for tag_dict in data:
+                # each release has an asset dict
+                for asset_dict in tag_dict.get('assets', []):
+                    # there is a direct download link for each asset, which should make the typical pattern for an HTML user
+                    download_url = asset_dict['browser_download_url']
+                    re_match = link_re.search(download_url)
+
+                    if re_match:
+                        # this one matches the pattern
+                        # link - just copy the download_url in full
+                        # version - pull out of the regex match
+                        data = re_match.groupdict()
+                        matches.append({
+                            'link' : download_url,
+                            'version' : data['version']
+                        })
+
+        # now strip down to the version(s) that are more recent than what currently is in bioconda
+        num = None
+        for num, match in enumerate(matches):
+            if match["version"] == self.vals["version"]:
+                break
+        if num is None:
+            return matches
+        return matches[:num + 1]
 
 class GithubTag(GithubBase):
     """Matches GitHub repository archives created automatically from tags"""

test/test_bioconductor_skeleton.py

@@ -98,7 +98,7 @@ def test_meta_contents(tmpdir, bioc_fetch):
 @pytest.mark.skip(reason="Does not currently work inside of the CI (cannot find the release) although it seems to work fine locally.")
 def test_find_best_bioc_version():
 
-    assert bioconductor_skeleton.find_best_bioc_version('DESeq2', '1.36.0') == '3.15'
+    assert bioconductor_skeleton.find_best_bioc_version('DESeq2', '1.40.1') == '3.17'
 
     # Non-existent version:
     with pytest.raises(bioconductor_skeleton.PackageNotFoundError):