Merge branch 'master' into support-exclude

bioconda_utils/bioconductor_skeleton.py

@@ -774,7 +774,7 @@ def dependencies(self):
                 dependency_mapping[prefix + name.lower() + version] = name
 
         # Check SystemRequirements in the DESCRIPTION file to make sure
-        # packages with such reqquirements are provided correct recipes.
+        # packages with such requirements are provided correct recipes.
         if (self.packages[self.package].get('SystemRequirements') is not None):
             logger.warning(
                 "The 'SystemRequirements' {} are needed".format(
@@ -940,7 +940,7 @@ def sub_placeholders(x):
         additional_run_deps = []
         if self.is_data_package:
             additional_run_deps.append('curl')
-            additional_run_deps.append('bioconductor-data-packages>={}'.format(date.today().strftime('%Y%m%d')))
+            additional_run_deps.append('bioconductor-data-packages >={}'.format(date.today().strftime('%Y%m%d')))
 
         d = OrderedDict((
             (
@@ -959,6 +959,7 @@ def sub_placeholders(x):
                 'build', OrderedDict((
                     ('number', self.build_number),
                     ('rpaths', ['lib/R/lib/', 'lib/']),
+                    ('run_exports', f'{{{{ pin_subpackage("bioconductor-{self.package_lower}", max_pin="x.x") }}}}'),
                 )),
             ),
             (
@@ -1248,7 +1249,19 @@ def write_recipe(package, recipe_dir, config, bioc_data_packages=None, force=Fal
             (updated_version == current_version) and
             (updated_meta != current_meta)
         ):
-            proj.build_number = int(current_build_number) + 1
+            # Sometimes when updating all packages, the updating process fails
+            # partway. Re-running the updating process should not bump the
+            # build number if no builds for this version exist yet in the repo.
+            existing_bldnos = utils.RepoData().get_package_data(
+                key="build_number",
+                name="bioconductor-" + proj.package.lower(),
+                version=updated_version
+            )
+            if not existing_bldnos:
+                proj.build_number = 0
+            else:
+                proj.build_number = sorted([int(i) for i in existing_bldnos]) [-1] + 1
+
         if 'extra' in current_meta:
             exclude = set(['final', 'copy_test_source_files'])
             proj.extra = {x: y for x, y in current_meta['extra'].items() if x not in exclude}

bioconda_utils/build_failure.py

@@ -38,6 +38,8 @@ def __init__(self, recipe: Union[str, Recipe], platform: Optional[str]=None):
         self.platform = platform
 
         def load(path):
+            if os.path.getsize(path) == 0:
+                raise IOError("Unable to read build failure record {path}: empty file")
             with open(path, "r") as f:
                 yaml=YAML()
                 try:
@@ -89,20 +91,26 @@ def write(self):
         with open(self.path, "w") as f:
             yaml=YAML()
             commented_map = CommentedMap()
-            commented_map.insert(0, "recipe_sha", self.recipe_sha, comment="The commit at which this recipe failed to build.")
+            commented_map.insert(0, "recipe_sha", self.recipe_sha, comment="The hash of the recipe's meta.yaml at which this recipe failed to build.")
             commented_map.insert(1, "skiplist", self.skiplist, comment="Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.")
             i = 2
-            if self.log:
+
+            _log = self.inner.get("log", "")
+            if _log:
                 commented_map.insert(
                     i,
                     "log", 
                     # remove invalid chars and keep only the last 100 lines
-                    LiteralScalarString("\n".join(utils.yaml_remove_invalid_chars(self.log).splitlines()[-100:])),
+                    LiteralScalarString("\n".join(utils.yaml_remove_invalid_chars(_log).splitlines()[-100:])),
                     comment="Last 100 lines of the build log."
                 )
                 i += 1
             if self.reason:
                 commented_map.insert(i, "reason", LiteralScalarString(self.reason))
+                i += 1
+            if self.category:
+                commented_map.insert(i, "category", LiteralScalarString(self.category))
+                i += 1
             yaml.dump(commented_map, f)
 
     def remove(self):

bioconda_utils/bulk.py

@@ -8,7 +8,7 @@
 def check_branch():
     branch = utils.run(["git", "rev-parse", "--abbrev-ref", "HEAD"], mask=False).stdout
     if branch != "bulk":
-        logger.error("bulk-run-ci has to be executed on a checkout of the bulk branch")
+        logger.error("bulk-trigger-ci has to be executed on a checkout of the bulk branch")
         exit(1)
 
 

bioconda_utils/cli.py

@@ -572,9 +572,7 @@ def dag(recipe_folder, config, packages="*", format='gml', hide_singletons=False
     """
     Export the DAG of packages to a graph format file for visualization
     """
-    dag, name2recipes = graph.build(utils.get_recipes(recipe_folder, "*"), config)
-    if packages != "*":
-        dag = graph.filter(dag, packages)
+    dag, name2recipes = graph.build(utils.get_recipes(recipe_folder, packages), config)
     if hide_singletons:
         for node in nx.nodes(dag):
             if dag.degree(node) == 0:
@@ -1104,15 +1102,11 @@ def list_build_failures(recipe_folder, config, channel=None, output_format=None,
     fmt_writer(df, sys.stdout, index=False)
 
 
-@arg(
-    'message',
-     help="The commit message. Will be prepended with [ci skip] to avoid that commits accidentally trigger a rerun while bulk is already running"
-)
-def bulk_commit(message):
-    bulk.commit(message)
-
-
 def bulk_trigger_ci():
+    """
+    Create an empty commit with the string "[ci run]" and push, which
+    triggers a bulk CI run. Must be on the `bulk` branch.
+    """
     bulk.trigger_ci()
 
 
@@ -1124,5 +1118,5 @@ def main():
         build, dag, dependent, do_lint, duplicates, update_pinning,
         bioconductor_skeleton, clean_cran_skeleton, autobump,
         handle_merged_pr, annotate_build_failures, list_build_failures,
-        bulk_commit, bulk_trigger_ci
+        bulk_trigger_ci
     ])