Fix env.spec update in manifest branch (#29)

* Fix env.spec update in manifest branch

.travis.yml

@@ -25,6 +25,7 @@ install:
 
     # Now do the things we need to do to install it.
     - conda install --file requirements.txt nose mock python=${PYTHON} --yes --quiet -c conda-forge
+    - conda list
     - python setup.py install
 
 script:

conda_gitenv/deploy.py

@@ -74,8 +74,14 @@ def create_env(pkgs, target, pkg_cache):
             # The downside is that we are not verifying that each package is installed correctly.
             return
 
+        try:
+            # Support conda>4.1
+            from conda.models.channel import prioritize_channels
+        except ImportError:
+            prioritize_channels = lambda nop: nop
+
         for source, pkg in pkgs:
-            index = conda.fetch.fetch_index([source], use_cache=False)
+            index = conda.fetch.fetch_index(prioritize_channels([source]), use_cache=False)
             # Deal with the fact that a recent conda includes the source in the index key.
             index = {pkg['fn']: pkg for pkg in index.values()}
 
@@ -103,16 +109,28 @@ def create_env(pkgs, target, pkg_cache):
                 conda.install.link(target, schannel_dist_name)
 
 
-def deploy_repo(repo, target, desired_env_labels=('*')):
+def deploy_repo(repo, target, desired_env_labels=None):
+    # Set pkgs_dirs location to be the specified pkg_cache.
     # Cache settings to be reinstated at the end.
+    import conda
     orig_package_cache_ = conda.install.package_cache_
-    orig_pkgs_dirs = conda.install.pkgs_dirs
+    pkg_cache = os.path.join(target, '.pkg_cache')
+    try:
+        # Support conda=4.1.*
+        orig_pkgs_dirs = conda.install.pkgs_dirs
+        conda.install.pkgs_dirs = [pkg_cache]
+    except AttributeError:
+        # Support conda>4.1
+        @property
+        def mocker(self):
+            return [pkg_cache]
+        import conda.base.context
+        orig_pkgs_dirs = conda.base.context.Context.pkgs_dirs
+        # Monkey patch the context instance property.
+        conda.base.context.Context.pkgs_dirs = mocker
 
     # Empty package cache so that it will reinitialised.
     conda.install.package_cache_ = {}
-    # Set pkgs_dirs location to be the specified pkg_cache.
-    pkg_cache = os.path.join(target, '.pkg_cache')
-    conda.install.pkgs_dirs = [pkg_cache]
 
     env_tags = tags_by_env(repo)
     for branch in repo.branches:
@@ -135,6 +153,8 @@ def deploy_repo(repo, target, desired_env_labels=('*')):
 
             # Only deploy environments that match the given pattern.
             labelled_tags = {}
+            if desired_env_labels is None:
+                desired_env_labels = ['*']
             for label, tag in all_labelled_tags.items():
                 if any([fnmatch.fnmatch('{}/{}'.format(branch.name, label),
                                         env_label) for env_label in desired_env_labels]):
@@ -158,7 +178,11 @@ def deploy_repo(repo, target, desired_env_labels=('*')):
                         os.symlink(label_target, label_location)
 
     conda.install.package_cache_ = orig_package_cache_
-    conda.install.pkgs_dirs = orig_pkgs_dirs
+    if isinstance(orig_pkgs_dirs, property):
+        # Support conda>4.1
+        conda.base.context.Context.pkgs_dirs = orig_pkgs_dirs
+    else:
+        conda.install.pkgs_dirs = orig_pkgs_dirs
 
 
 def configure_parser(parser):

conda_gitenv/lock.py

@@ -14,4 +14,6 @@ def __init__(self, directory_to_lock):
         """
         dirname, basename = os.path.split(directory_to_lock.rstrip(os.pathsep))
         path = os.path.join(dirname, '.conda-lock_' + basename)
+        if not os.path.isdir(dirname):
+            os.makedirs(dirname)
         return conda.lock.Locked.__init__(self, path)

conda_gitenv/resolve.py

@@ -60,6 +60,9 @@ def build_manifest_branches(repo):
             continue
         with open(spec_fname, 'r') as fh:
             pkgs = resolve_spec(fh)
+            # Cache the contents of the env.spec file from the source branch.
+            fh.seek(0)
+            spec_lines = fh.readlines()
         manifest_branch_name = '{}{}'.format(manifest_branch_prefix, name)
         if manifest_branch_name in repo.branches:
             manifest_branch = repo.branches[manifest_branch_name]
@@ -69,7 +72,10 @@ def build_manifest_branches(repo):
         manifest_path = os.path.join(repo.working_dir, 'env.manifest')
         with open(manifest_path, 'w') as fh:
             fh.write('\n'.join(pkgs))
-        repo.index.add([manifest_path])
+        # Write the env.spec from the source branch into the manifest branch.
+        with open(spec_fname, 'w') as fh:
+            fh.writelines(spec_lines)
+        repo.index.add([manifest_path, spec_fname])
         if repo.is_dirty():
             repo.index.commit('Manifest update from {:%Y-%m-%d %H:%M:%S}.'
                               ''.format(datetime.datetime.now()))

conda_gitenv/tests/integration/setup_samples.py

@@ -23,18 +23,20 @@ def add_env(repo, name, spec):
     return branch
 
 
-def update_env(repo, branch, spec):
+def update_env(repo, branch, spec, comment=None):
     branch.checkout()
     env_spec = os.path.join(repo.working_dir, 'env.spec')
     with open(env_spec, 'w') as fh:
         fh.write(textwrap.dedent(spec))
     repo.index.add([env_spec])
-    repo.index.commit('Add {} spec'.format(branch.name))
+    if comment is None:
+        comment = 'Add {} spec'.format(branch.name)
+    repo.index.commit(comment)
 
 
-def basic_repo():
+def basic_repo(name='basic'):
     # The simplest kind of repo. One env defined under the name "master"
-    repo = create_repo('basic')
+    repo = create_repo(name)
     branch = add_env(repo, 'master', """
         env:
          - python

conda_gitenv/tests/integration/test_resolve.py

@@ -8,18 +8,48 @@
 
 
 class Test_full_build(unittest.TestCase):
-    def test_basic_env(self):
-        repo = setup_samples.basic_repo()
+    def check_env(self, name):
+        repo = setup_samples.basic_repo(name)
         self.assertNotIn('manifest/master', repo.branches)
         check_call(['conda', 'gitenv', 'resolve', repo.working_dir])
         self.assertIn('manifest/master', repo.branches)
         manifest_branch = repo.branches['manifest/master']
         manifest_branch.checkout()
         with open(os.path.join(repo.working_dir, 'env.manifest'), 'r') as fh:
-            manifest_contents = fh.readlines()
-            pkg_names = [pkg.split('\t', 1)[1].split('-')[0] for pkg in manifest_contents]
+            env_manifest = fh.readlines()
+            pkg_names = [pkg.split('\t', 1)[1].split('-')[0]
+                         for pkg in env_manifest]
             self.assertIn('python', pkg_names)
             self.assertIn('zlib', pkg_names)
+        return repo
+
+    def test_env_basic(self):
+        self.check_env('basic')
+
+    def test_env_update(self):
+        repo = self.check_env('update')
+        master = repo.branches['master']
+        spec = """
+            env:
+             - python
+             - numpy
+            channels:
+             - defaults
+            """
+        comment = 'Update the env.spec'
+        setup_samples.update_env(repo, master, spec, comment)
+        self.assertIn('manifest/master', repo.branches)
+        check_call(['conda', 'gitenv', 'resolve', repo.working_dir])
+        manifest = repo.branches['manifest/master']
+        manifest.checkout()
+        with open(os.path.join(repo.working_dir, 'env.manifest'), 'r') as fh:
+            env_manifest = fh.readlines()
+            pkg_names = [pkg.split('\t', 1)[1].split('-')[0]
+                         for pkg in env_manifest]
+            self.assertIn('numpy', pkg_names)
+        with open(os.path.join(repo.working_dir, 'env.spec'), 'r') as fh:
+            env_spec = [entry.strip() for entry in fh.readlines()]
+        self.assertIn('- numpy', env_spec)
 
 
 if __name__ == '__main__':

requirements.txt

@@ -1,5 +1,5 @@
 gitpython
 pyyaml
-conda-build-all
+conda-build-all !=1.0.2
 conda-build ==2.0.6
-requests !=2.12.0
+requests <2.12.0