From 3ea279915e0958ba896782235e0be362a46abf9c Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:29:45 -0600
Subject: [PATCH 01/18] Bot: Add lint fix command

---
 bioconda_utils/bot/commands.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/bioconda_utils/bot/commands.py b/bioconda_utils/bot/commands.py
index e6ac38b5e2..ce039dbc37 100644
--- a/bioconda_utils/bot/commands.py
+++ b/bioconda_utils/bot/commands.py
@@ -117,8 +117,18 @@ async def command_bump(ghapi, issue_number, _user, *_args):
 
 
 @command_routes.register("lint")
-async def command_lint(ghapi, issue_number, _user, *_args):
-    """Lint the current recipe"""
+async def command_lint(ghapi, issue_number, _user, *args):
+    """Lint the current recipe
+
+    If the additional argument ``fix`` is provided, an attempt to fix errors
+    will be scheduled instead of a new check run. This is identical to clicking
+    the "Fix Issues" button on the checks page.
+    """
+    if args:
+        if args[0] == 'fix':
+            pr = await ghapi.get_prs(number=issue_number)
+            tasks.lint_fix.s(None, pr['head']['sha'], ghapi).apply_async()
+            return f"Scheduled fixing lints in #{issue_number}"
     (
         tasks.get_latest_pr_commit.s(issue_number, ghapi) |
         tasks.create_check_run.s(ghapi)

From 76bb9994bfb24d4ef6e405df34a4eebc7f501bbb Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:33:07 -0600
Subject: [PATCH 02/18] Bot: detect branch name when running from SHA only

This should fix committing lint fixes.
---
 bioconda_utils/bot/tasks.py  |  2 +-
 bioconda_utils/githandler.py | 11 +++++++++++
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/bioconda_utils/bot/tasks.py b/bioconda_utils/bot/tasks.py
index 3d506247d4..f1e9c4abbf 100644
--- a/bioconda_utils/bot/tasks.py
+++ b/bioconda_utils/bot/tasks.py
@@ -92,7 +92,7 @@ async def __aenter__(self):
             elif self.ref:
                 fork_user = None
                 fork_repo = None
-                branch_name = "unknown"
+                branch_name = None
                 ref = self.ref
             elif self.branch_name:
                 fork_user = None
diff --git a/bioconda_utils/githandler.py b/bioconda_utils/githandler.py
index 6c3f780a97..ad5d5cffda 100644
--- a/bioconda_utils/githandler.py
+++ b/bioconda_utils/githandler.py
@@ -218,6 +218,14 @@ def get_remote_branch(self, branch_name: str, try_fetch=False):
             return None
         for remote_ref in remote_refs:
             if remote_ref.remote_ref_path == branch_name:
+                remote_heads = [head for head in self.fork_remote.refs
+                                if head.commit.hexsha == branch_name]
+                if remote_heads:
+                    if len(remote_heads) > 1:
+                        logger.warning("Found multiple heads for %s - using %s",
+                                       branch_name, remote_heads[0])
+                        logger.warning("  other options: %s", remote_heads[1:])
+                    return remote_heads[0]
                 return remote_ref.ref
 
     def get_latest_master(self):
@@ -249,6 +257,9 @@ def create_local_branch(self, branch_name: str, remote_branch: str = None):
             remote_branch = self.get_remote_branch(remote_branch, try_fetch=False)
         if remote_branch is None:
             return None
+        if branch_name is None:
+            branch_name = remote_branch.remote_head
+            logger.info("Resolved %s to %s", remote_branch, branch_name)
         self.repo.create_head(branch_name, remote_branch)
         return self.get_local_branch(branch_name)
 

From a415d0410aae929e9fe301530f00ef43b425b8e1 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:33:58 -0600
Subject: [PATCH 03/18] Git: Allow setting cache dir from env (for faster
 debug)

---
 bioconda_utils/githandler.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/bioconda_utils/githandler.py b/bioconda_utils/githandler.py
index ad5d5cffda..984e17e35d 100644
--- a/bioconda_utils/githandler.py
+++ b/bioconda_utils/githandler.py
@@ -543,8 +543,15 @@ class TempGitHandler(GitHandlerBase):
     might be working in multiple threads and want to avoid blocking waits for
     a single repo. It also improves robustness: If something goes wrong with this
     repo, it will not break the entire process.
-    """
 
+    This class uses a bare clone as a cache to speed up subsequent
+    instantiations of temporary git clones. This bare "caching" clone
+    will be created in a temporary directory. To save on download
+    times when debugging, you can use the environment variable
+    ``BIOCONDA_REPO_CACHEDIR`` to specify a directory lasting accross
+    instantiations of the Python interpreter.
+
+    """
     _local_mirror_tmpdir: Union[str, tempfile.TemporaryDirectory] = None
 
     @classmethod
@@ -669,3 +676,7 @@ class BiocondaRepo(GitHandler, BiocondaRepoMixin):
 
 class TempBiocondaRepo(TempGitHandler, BiocondaRepoMixin):
     pass
+
+
+# Allow setting a pre-checkout from env
+TempGitHandler.set_mirror_dir(os.environ.get('BIOCONDA_REPO_CACHEDIR'))

From d54d24af402d9b49538615584659a0790e6eb544 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:34:27 -0600
Subject: [PATCH 04/18] Git: fix https:// not stripped if no password

---
 bioconda_utils/githandler.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bioconda_utils/githandler.py b/bioconda_utils/githandler.py
index 984e17e35d..8a4d72b29d 100644
--- a/bioconda_utils/githandler.py
+++ b/bioconda_utils/githandler.py
@@ -588,6 +588,7 @@ def _get_local_mirror(cls, url: str) -> git.Repo:
 
         # Make location of repo in tmpdir from url
         _, _, fname = url.rpartition('@')
+        fname = fname.lstrip('https://')
         tmpname = getattr(cls._local_mirror_tmpdir, 'name', cls._local_mirror_tmpdir)
         mirror_name = os.path.join(tmpname, fname)
 

From 67da9dbfc06d32e872d3f3f3815f56d1ae87c6a5 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:34:53 -0600
Subject: [PATCH 05/18] Git: add keep_tempdir() to TempGitHandler

---
 bioconda_utils/githandler.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/bioconda_utils/githandler.py b/bioconda_utils/githandler.py
index 8a4d72b29d..a97bd6eadd 100644
--- a/bioconda_utils/githandler.py
+++ b/bioconda_utils/githandler.py
@@ -8,6 +8,7 @@
 import tempfile
 import subprocess
 from typing import List, Union
+import shutil
 
 import git
 import yaml
@@ -631,6 +632,8 @@ def __init__(self,
                  fork_user=None,
                  fork_repo=None,
                  dry_run=False) -> None:
+        self._clean = True
+
         userpass = ""
         if password is not None and username is None:
             username = "x-access-token"
@@ -664,12 +667,19 @@ def censor(string):
         logger.info("Finished setting up repo in %s", self.tempdir)
         super().__init__(repo, dry_run, home_url, fork_url)
 
+    def keep_tempdir(self):
+        """Disable temp dir removal on `close`"""
+        self._clean = False
 
     def close(self) -> None:
         """Remove temporary clone and cleanup resources"""
         super().close()
-        logger.info("Removing repo from %s", self.tempdir.name)
-        self.tempdir.cleanup()
+        if self._clean:
+            logger.info("Removing repo from %s", self.tempdir.name)
+            self.tempdir.cleanup()
+        else:
+            logger.warning("Keeping repo in %s%s", self.tempdir.name, "_saved")
+            shutil.copytree(self.tempdir.name, self.tempdir.name + "_saved")
 
 
 class BiocondaRepo(GitHandler, BiocondaRepoMixin):

From a6e6c6e848ab4d3c64586c362d19a6ff84635cfb Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:36:58 -0600
Subject: [PATCH 06/18] Bot: fix unhandled check_run action is not an error

---
 bioconda_utils/bot/events.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bioconda_utils/bot/events.py b/bioconda_utils/bot/events.py
index 799d846058..210061d31b 100644
--- a/bioconda_utils/bot/events.py
+++ b/bioconda_utils/bot/events.py
@@ -109,7 +109,7 @@ async def handle_check_run(event, ghapi):
         else:
             logger.error("Unknown requested action in check run: %s", requested_action)
     else:
-        logger.error("Unknown action %s", action)
+        logger.info("Action '%s' unhandled", action)
 
 @event_routes.register("pull_request")
 async def handle_pull_request(event, ghapi):

From 4db4d62204f7a8e5be4cbaf0115abda7b3788685 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 12:38:51 -0600
Subject: [PATCH 07/18] Github: fix leftover error log message

---
 bioconda_utils/githubhandler.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bioconda_utils/githubhandler.py b/bioconda_utils/githubhandler.py
index 4caebc3166..3d5c9beb8e 100644
--- a/bioconda_utils/githubhandler.py
+++ b/bioconda_utils/githubhandler.py
@@ -359,7 +359,6 @@ async def get_prs_from_sha(self, head_sha: str, only_open=False) -> List[int]:
                                           closed=False if only_open else None)
         for pull in result.get('items', []):
             pr_number = int(pull['number'])
-            logger.error("checking %s", pr_number)
             full_pr = await self.get_prs(number=pr_number)
             if full_pr['head']['sha'].startswith(head_sha):
                 pr_numbers.append(pr_number)

From 26030999d8c370983a72687b7ff7b9de3ef4a86b Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 13:48:21 -0600
Subject: [PATCH 08/18] Github: catch exception if branch to delete does not
 exist

---
 bioconda_utils/githubhandler.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/bioconda_utils/githubhandler.py b/bioconda_utils/githubhandler.py
index 3d5c9beb8e..b85cce19a6 100644
--- a/bioconda_utils/githubhandler.py
+++ b/bioconda_utils/githubhandler.py
@@ -893,7 +893,7 @@ async def get_contents(self, path: str, ref: str = None) -> str:
         content = content_bytes.decode('utf-8')
         return content
 
-    async def delete_branch(self, ref: str) -> None:
+    async def delete_branch(self, ref: str) -> bool:
         """Delete a branch (ref)
 
         Arguments:
@@ -901,7 +901,12 @@ async def delete_branch(self, ref: str) -> None:
         """
         var_data = copy(self.var_default)
         var_data['ref'] = ref
-        await self.api.delete(self.GIT_REFERENCE, var_data)
+        try:
+            await self.api.delete(self.GIT_REFERENCE, var_data)
+            return True
+        except gidgethub.InvalidField as exc:
+            logger.info("Failed to delete branch %s: %s", ref, exc)
+            return False
 
     def _deparse_card_pr_number(self, card: Dict[str, Any]) -> Dict[str, Any]:
         """Extracts the card's issue's number from the content_url

From 1f09697188008d035cae2b3021b22bc675115bd7 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 13:48:53 -0600
Subject: [PATCH 09/18] Bot: log when we try to delete branch

---
 bioconda_utils/bot/tasks.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bioconda_utils/bot/tasks.py b/bioconda_utils/bot/tasks.py
index f1e9c4abbf..c2c12febcd 100644
--- a/bioconda_utils/bot/tasks.py
+++ b/bioconda_utils/bot/tasks.py
@@ -570,7 +570,9 @@ async def merge_pr(self, pr_number: int, comment_id: int, ghapi) -> Tuple[bool,
         return res, msg
 
     if not branch.startswith('pull/'):
+        logger.info("Trying to delete branch %s", branch)
         await ghapi.delete_branch(branch)
+
     return res, msg
 
 

From 8eafd5245b2ecedde4147678892ff19e81beb045 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 13:55:43 -0600
Subject: [PATCH 10/18] Bot: fix deleting branch after merge (hopefully)

---
 bioconda_utils/bot/tasks.py | 30 ++++++++++++++++++------------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/bioconda_utils/bot/tasks.py b/bioconda_utils/bot/tasks.py
index c2c12febcd..7c308831cc 100644
--- a/bioconda_utils/bot/tasks.py
+++ b/bioconda_utils/bot/tasks.py
@@ -442,23 +442,23 @@ async def merge_pr(self, pr_number: int, comment_id: int, ghapi) -> Tuple[bool,
     head_ref = pr['head']['ref']
     head_sha = pr['head']['sha']
     head_user = pr['head']['repo']['owner']['login']
-    # get path for Circle
+
+    # get artifacts from circleci
     if head_user == ghapi.user:
-        branch = head_ref
+        circle_path = head_ref
     else:
-        branch = "pull/{}".format(pr_number)
+        circle_path = "pull/{}".format(pr_number)
+    capi = AsyncCircleAPI(ghapi.session, token=CIRCLE_TOKEN)
+    artifacts = await capi.get_artifacts(circle_path, head_sha)
 
     lines = []
-
-    capi = AsyncCircleAPI(ghapi.session, token=CIRCLE_TOKEN)
-    artifacts = await capi.get_artifacts(branch, head_sha)
     files = []
     images = []
     packages = []
-    for path, url, buildno in artifacts:
+    for path, url, _buildno in artifacts:
         match = PACKAGE_RE.match(url)
         if match:
-            repo_url, arch, fname = match.groups()
+            _repo_url, arch, fname = match.groups()
             fpath = os.path.join(arch, fname)
             files.append((url, fpath))
             packages.append(fpath)
@@ -483,7 +483,7 @@ async def merge_pr(self, pr_number: int, comment_id: int, ghapi) -> Tuple[bool,
         try:
             fds = []
             urls = []
-            for url,path in files:
+            for url, path in files:
                 fpath = os.path.join(tmpdir, path)
                 fdir = os.path.dirname(fpath)
                 if not os.path.exists(fdir):
@@ -569,9 +569,15 @@ async def merge_pr(self, pr_number: int, comment_id: int, ghapi) -> Tuple[bool,
     if not res:
         return res, msg
 
-    if not branch.startswith('pull/'):
-        logger.info("Trying to delete branch %s", branch)
-        await ghapi.delete_branch(branch)
+    if head_user == ghapi.user:
+        # PR head branch is on same account as our install - it's a PR not
+        # from a fork. Go ahead and try to delete the branch.
+        if head_ref in ('master', 'bulk'):
+            # Safeguard - never delete master or bulk!
+            logger.error("Cowardly refusing to delete master or bulk")
+        else:
+            logger.info("Trying to delete branch %s", head_ref)
+            await ghapi.delete_branch(head_ref)
 
     return res, msg
 

From a846bd375ecb97e6be004d86bfef9bccf37688ee Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 18:03:34 -0600
Subject: [PATCH 11/18] Recipe: fix fence post error

---
 bioconda_utils/recipe.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bioconda_utils/recipe.py b/bioconda_utils/recipe.py
index da1596548a..d264237775 100644
--- a/bioconda_utils/recipe.py
+++ b/bioconda_utils/recipe.py
@@ -415,7 +415,7 @@ def get_raw_range(self, path):
           a tuple of first_row, first_column, last_row, last_column
         """
         if not path:
-            return 0, 0, len(self.meta_yaml), len(self.meta_yaml[-1])
+            return 0, 0, len(self.meta_yaml)-1, len(self.meta_yaml[-1])
 
         nodes, keys = self._walk(path)
         nodes.pop()  # pop parsed value
@@ -524,10 +524,10 @@ def set(self, path, value):
             _, col, row, _ = self.get_raw_range(found_path)
             backup = deepcopy(self.meta_yaml)
             for key in path.split('/')[len(keys):]:
-                self.meta_yaml.insert(row, ' ' * col + key + ':')
+                self.meta_yaml.insert(row + 1, ' ' * col + key + ':')
                 row += 1
                 col += 2
-            self.meta_yaml[row-1] += " marker"
+            self.meta_yaml[row] += " None"
             self.render()
 
         # get old content

From f48a31aba6a244f04fa2ac55d777a480d40f8dc9 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 18:05:07 -0600
Subject: [PATCH 12/18] Recipe: add has_selector()

---
 bioconda_utils/recipe.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/bioconda_utils/recipe.py b/bioconda_utils/recipe.py
index d264237775..228611060e 100644
--- a/bioconda_utils/recipe.py
+++ b/bioconda_utils/recipe.py
@@ -146,6 +146,7 @@ class Recipe():
         "cdt": lambda x: x
     }
 
+    _selector_re = re.compile(r'# +\[.*\]')
 
     def __init__(self, recipe_dir, recipe_folder):
         if not recipe_dir.startswith(recipe_folder):
@@ -751,6 +752,17 @@ def conda_release(self):
             self._conda_tempdir.cleanup()
             self._conda_tempdir = None
 
+    def has_selector(self, section: str = '') -> bool:
+        """Checks if the recipe uses ``# [cond]`` line selectors
+
+        Args:
+          section: Limit check to section
+
+        """
+        if self._selector_re.search(self.get_raw(section)):
+            return True
+        return False
+
 
 def load_parallel_iter(recipe_folder, packages):
     recipes = list(utils.get_recipes(recipe_folder, packages))

From 594a1bff16cfd79c26b7a19cdd4b87667d48202c Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 22:42:18 -0600
Subject: [PATCH 13/18] Lint/test: fix keeping comments in keys added to test
 case

---
 test/conftest.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/test/conftest.py b/test/conftest.py
index 8e51b80e13..17844f55f5 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -97,14 +97,21 @@ def recipes_folder(tmpdir: py.path.local):
 
 
 def dict_merge(base, add):
+    """Merge **add** into **base**
+
+    Takes care to keep ruamel.yaml CommentedMap comments intact.
+    """
     for key, value in add.items():
         if isinstance(value, dict):
-            base[key] = dict_merge(base.get(key, {}), value)
+            base[key] = dict_merge(base.get(key, type(base)()), value)
         elif isinstance(base, list):
             for num in range(len(base)):
-                base[num][key] = dict_merge(base[num].get(key, {}), add)
+                base[num][key] = dict_merge(base[num].get(key, type(base[num])()), add)
         else:
             base[key] = value
+            if hasattr(add, 'copy_attributes') and \
+               hasattr(base, 'copy_attributes'):
+                add.copy_attributes(base)
     return base
 
 

From ece7eff0ab7a4623fe8ccb934e8d8fd2aab73492 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 22:51:17 -0600
Subject: [PATCH 14/18] Recipe: add noarch, dep and compiler checks

---
 bioconda_utils/recipe.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/bioconda_utils/recipe.py b/bioconda_utils/recipe.py
index 228611060e..cb4145ed65 100644
--- a/bioconda_utils/recipe.py
+++ b/bioconda_utils/recipe.py
@@ -763,6 +763,30 @@ def has_selector(self, section: str = '') -> bool:
             return True
         return False
 
+    def has_compiler(self) -> bool:
+        """Checks if the recipe uses a compiler"""
+        if any(dep.startswith('compiler_') for dep in self.get_deps()):
+               return True
+        return False
+
+    def is_noarch(self, python: bool =  None) -> bool:
+        """Checks if the recipe is marked noarch"""
+        noarch = self.get('build/noarch', False)
+        if python:
+            return noarch == 'python'
+        return noarch in (True, 'generic')
+
+    def has_dep(self, dep: str = None, section=None) -> bool:
+        """Checks if the recipe requires **dep**
+
+        Args:
+          dep: The dependency to check for or None
+          section: The section(s) the dep must occur in
+        """
+        if dep:
+            return dep in self.get_deps_dict(section)
+        return bool(self.get_deps_dict(section))
+
 
 def load_parallel_iter(recipe_folder, packages):
     recipes = list(utils.get_recipes(recipe_folder, packages))

From c5a6678d2678e70093c601021728b9fb06489f03 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 22:53:24 -0600
Subject: [PATCH 15/18] Lint/noarch: log fixes made

---
 bioconda_utils/lint/check_noarch.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/bioconda_utils/lint/check_noarch.py b/bioconda_utils/lint/check_noarch.py
index 3dca6d2598..65ce70a0b6 100644
--- a/bioconda_utils/lint/check_noarch.py
+++ b/bioconda_utils/lint/check_noarch.py
@@ -10,6 +10,10 @@
 
 from . import LintCheck, ERROR, WARNING, INFO
 
+from logging import getLogger
+
+logger = getLogger(__name__)
+
 
 # Noarch or not checks:
 #
@@ -22,6 +26,7 @@
 #   b) Not use ``- python [<>]3``,
 #      but use ``skip: True  # [py[23]k]``
 
+
 class should_be_noarch_python(LintCheck):
     """The recipe should be build as ``noarch``
 
@@ -47,6 +52,7 @@ def check_deps(self, deps):
         self.message(section='build', data=True)
 
     def fix(self, _message, _data):
+        logger.warning("Lint fix: setting build/noarch=python")
         self.recipe.set('build/noarch', 'python')
         return True
 
@@ -73,6 +79,7 @@ def check_deps(self, deps):
         self.message(section='build', data=True)
 
     def fix(self, _message, _data):
+        logger.warning("Lint fix: setting build/noarch=generic")
         self.recipe.set('build/noarch', 'generic')
         return True
 

From de8311b377889f2f127dc1bdfd93a13202357144 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 23:02:45 -0600
Subject: [PATCH 16/18] Recipe: fix is_noarch(python)

---
 bioconda_utils/recipe.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/bioconda_utils/recipe.py b/bioconda_utils/recipe.py
index cb4145ed65..bed1a85e10 100644
--- a/bioconda_utils/recipe.py
+++ b/bioconda_utils/recipe.py
@@ -770,11 +770,18 @@ def has_compiler(self) -> bool:
         return False
 
     def is_noarch(self, python: bool =  None) -> bool:
-        """Checks if the recipe is marked noarch"""
+        """Checks if the recipe is marked noarch
+
+        Args:
+          python: If true, checks for noarch python.
+                  If false, checks for noarch not python.
+        """
         noarch = self.get('build/noarch', False)
         if python:
             return noarch == 'python'
-        return noarch in (True, 'generic')
+        if python is False:
+            return noarch in (True, 'generic')
+        return noarch in (True, 'generic', 'python')
 
     def has_dep(self, dep: str = None, section=None) -> bool:
         """Checks if the recipe requires **dep**

From 437aa1bc8582263f7a3fe3f058770bfa409187ff Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 23:12:23 -0600
Subject: [PATCH 17/18] Lint: cleanup noarch tests

---
 bioconda_utils/lint/check_noarch.py | 78 ++++++++++++++---------------
 test/lint_cases.yaml                | 22 ++++++--
 2 files changed, 58 insertions(+), 42 deletions(-)

diff --git a/bioconda_utils/lint/check_noarch.py b/bioconda_utils/lint/check_noarch.py
index 65ce70a0b6..cb3ce6737c 100644
--- a/bioconda_utils/lint/check_noarch.py
+++ b/bioconda_utils/lint/check_noarch.py
@@ -41,15 +41,11 @@ class should_be_noarch_python(LintCheck):
 
     """
     def check_deps(self, deps):
-        if 'python' not in deps:
-            return  # not a python package
-        if all('build' not in loc for loc in deps['python']):
-            return  # only uses python in run/host
-        if any(dep.startswith('compiler_') for dep in deps):
-            return  # not compiled
-        if self.recipe.get('build/noarch', None) == 'python':
-            return  # already marked noarch: python
-        self.message(section='build', data=True)
+        if not self.recipe.is_noarch(python=True) and \
+           self.recipe.has_dep('python', section='host') and \
+           not self.recipe.has_compiler() and \
+           not self.recipe.has_selector():
+            self.message(section='build', data=True)
 
     def fix(self, _message, _data):
         logger.warning("Lint fix: setting build/noarch=python")
@@ -72,11 +68,13 @@ class should_be_noarch_generic(LintCheck):
     """
     requires = ['should_be_noarch_python']
     def check_deps(self, deps):
-        if any(dep.startswith('compiler_') for dep in deps):
-            return  # not compiled
-        if self.recipe.get('build/noarch', None):
-            return  # already marked noarch
-        self.message(section='build', data=True)
+        if not self.recipe.is_noarch(python=False) and \
+           not self.recipe.has_dep('python', section='host') and \
+           not self.recipe.has_compiler() and \
+           not self.recipe.has_selector():
+            logger.error("here")
+            logger.error(self.recipe.has_selector())
+            self.message(section='build', data=True)
 
     def fix(self, _message, _data):
         logger.warning("Lint fix: setting build/noarch=generic")
@@ -93,11 +91,8 @@ class should_not_be_noarch_compiler(LintCheck):
 
     """
     def check_deps(self, deps):
-        if not any(dep.startswith('compiler_') for dep in deps):
-            return  # not compiled
-        if self.recipe.get('build/noarch', False) is False:
-            return  # no noarch, or noarch=False
-        self.message(section='build/noarch')
+        if self.recipe.is_noarch() and self.recipe.has_compiler():
+            self.message(section='build/noarch')
 
 
 class should_not_be_noarch_skip(LintCheck):
@@ -107,11 +102,23 @@ class should_not_be_noarch_skip(LintCheck):
 
     """
     def check_recipe(self, recipe):
-        if self.recipe.get('build/noarch', False) is False:
-            return  # no noarch, or noarch=False
-        if self.recipe.get('build/skip', False) is False:
-            return  # no skip or skip=False
-        self.message(section='build/noarch')
+        if self.recipe.is_noarch() and \
+           self.recipe.get('build/skip', False) is not False:
+            self.message(section='build/noarch')
+
+
+class should_not_be_noarch_selector(LintCheck):
+    """The recipe uses ``# [cond]`` but is marked noarch
+
+    Recipes using conditional lines cannot be noarch.
+
+    """
+    requires = ['should_use_compilers',
+                'should_not_be_noarch_skip',
+                'should_not_be_noarch_source']
+    def check_recipe(self, recipe):
+        if self.recipe.is_noarch() and self.recipe.has_selector():
+            self.message(section='build/noarch')
 
 
 class should_not_use_skip_python(LintCheck):
@@ -134,16 +141,12 @@ class should_not_use_skip_python(LintCheck):
     bad_skip_terms = ('py2k', 'py3k', 'python')
 
     def check_deps(self, deps):
-        if 'python' not in deps:
-            return  # not a python package
-        if any(dep.startswith('compiler_') for dep in deps):
-            return  # not compiled
-        if self.recipe.get('build/skip', None) is None:
-            return  # no build: skip: section
-        skip_line = self.recipe.get_raw('build/skip')
-        if not any(term in skip_line for term in self.bad_skip_terms):
-            return  # no offending skip terms
-        self.message(section='build/skip')
+        if self.recipe.has_dep('python') and \
+           not self.recipe.has_compiler() and \
+           self.recipe.get('build/skip', None) is not None and \
+           any(term in self.bad_skip_terms
+               for term in self.recipe.get_raw('build/skip')):
+            self.message(section='build/skip')
 
 
 class should_not_be_noarch_source(LintCheck):
@@ -153,9 +156,6 @@ class should_not_be_noarch_source(LintCheck):
     platform. Remove the noarch section or use just one source for all
     platforms.
     """
-
-    _pat = re.compile(r'# +\[.*\]')
     def check_source(self, source, section):
-        # just search the entire source entry for a comment
-        if self._pat.search(self.recipe.get_raw(f"{section}")):
-             self.message(section)
+        if self.recipe.is_noarch() and self.recipe.has_selector(section):
+            self.message(section)
diff --git a/test/lint_cases.yaml b/test/lint_cases.yaml
index 6c33a933cf..a6d21c71d0 100644
--- a/test/lint_cases.yaml
+++ b/test/lint_cases.yaml
@@ -191,10 +191,10 @@ tests:
   expect: has_windows_bat_file
 # FIXME: should_be_noarch without python
 - name: should_be_noarch_python
-  add: { requirements: { build: [python], run: [python] } }
+  add: { requirements: { host: [python], run: [python] } }
   expect: should_be_noarch_python
 - name: should_be_noarch_python_good
-  add: { build: { noarch: python }, requirements: { build: [python], run: [python] } }
+  add: { build: { noarch: python }, requirements: { host: [python], run: [python] } }
 - name: should_be_noarch_python_good_skip
   add:
     build: { noarch: python, skip: false }
@@ -204,12 +204,18 @@ tests:
     build: { noarch: python }
     requirements: { build: [compiler_gcc]}
   expect: should_not_be_noarch_compiler
-- name: should_not_be_noarch_skip
+- name: should_not_be_noarch_python_skip
   add:
     build:
       noarch: python
       skip: True  # [osx]
   expect: should_not_be_noarch_skip
+- name: should_not_be_noarch_generic_skip
+  add:
+    build:
+      noarch: generic
+      skip: True  # [osx]
+  expect: should_not_be_noarch_skip
 - name: should_not_be_noarch_source
   expect: should_not_be_noarch_source
   remove: source
@@ -219,6 +225,16 @@ tests:
         sha256: 123
       - url: https://elsewhere  # [osx]
         sha256: 123
+- name: should_not_be_noarch_source_good
+  remove: source
+  add:
+    build:
+      noarch: False
+    source:
+      - url: https://somewhere  # [linux]
+        sha256: 123
+      - url: https://elsewhere  # [osx]
+        sha256: 123
 - name: noarch_java_with_python_wrapper
   add:
     build: { noarch: generic }

From 0d88d6cd66fd48f079792adc130fa69449652d1a Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <elmar.pruesse@ucdenver.edu>
Date: Sun, 30 Jun 2019 23:24:12 -0600
Subject: [PATCH 18/18] Git: fix symbolicreference has no remote_head

---
 bioconda_utils/githandler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bioconda_utils/githandler.py b/bioconda_utils/githandler.py
index a97bd6eadd..39a77e05b5 100644
--- a/bioconda_utils/githandler.py
+++ b/bioconda_utils/githandler.py
@@ -258,7 +258,7 @@ def create_local_branch(self, branch_name: str, remote_branch: str = None):
             remote_branch = self.get_remote_branch(remote_branch, try_fetch=False)
         if remote_branch is None:
             return None
-        if branch_name is None:
+        if branch_name is None and hasattr(remote_branch, 'remote_head'):
             branch_name = remote_branch.remote_head
             logger.info("Resolved %s to %s", remote_branch, branch_name)
         self.repo.create_head(branch_name, remote_branch)