adding in environmental variable to pkg_test

bioconda_utils/build.py

@@ -34,6 +34,7 @@ def build(
     force=False,
     channels=None,
     docker_builder=None,
+    mulled_upload_target='biocontainers',
 ):
     """
     Build a single recipe for a single env
@@ -66,6 +67,10 @@ def build(
     docker_builder : docker_utils.RecipeBuilder object
         Use this docker builder to build the recipe, copying over the built
         recipe to the host's conda-bld directory.
+
+    mulled_upload_target: biocontainers 
+        Namespace for docker container
+
     """
 
     # Clean provided env and exisiting os.environ to only allow whitelisted env
@@ -161,7 +166,10 @@ def build(
     base_image = 'bioconda/extended-base-image' if use_base_image else None
 
     try:
-        res = pkg_test.test_package(pkg_path, base_image=base_image)
+        if channels:
+            res = pkg_test.test_package(pkg_path, base_image=base_image, mulled_upload_target=mulled_upload_target, channels=channels)
+        else:
+            res = pkg_test.test_package(pkg_path, base_image=base_image, mulled_upload_target=mulled_upload_target)
 
         logger.info("TEST SUCCESS %s, %s", recipe, utils.envstr(_env))
         mulled_image = pkg_test.get_image_name(pkg_path)
@@ -181,7 +189,7 @@ def build_recipes(
     docker_builder=None,
     label=None,
     anaconda_upload=False,
-    mulled_upload_target=None,
+    mulled_upload_target='biocontainers',
     check_channels=None,
 ):
     """
@@ -222,7 +230,7 @@ def build_recipes(
     anaconda_upload :  bool
         If True, upload the package to anaconda.org.
 
-    mulled_upload_target : None
+    mulled_upload_target : biocontainers
         If not None, upload the mulled docker image to the given target on quay.io.
 
     check_channels : list
@@ -350,6 +358,7 @@ def build_recipes(
                 force=force,
                 channels=config['channels'],
                 docker_builder=docker_builder,
+                mulled_upload_target=mulled_upload_target,
             )
 
             all_success &= res.success

bioconda_utils/cli.py

@@ -346,7 +346,7 @@ def build(
     build_script_template=None,
     pkg_dir=None,
     anaconda_upload=False,
-    mulled_upload_target=None,
+    mulled_upload_target='biocontainers',
     keep_image=False,
 ):
     setup_logger(loglevel)

bioconda_utils/docker_utils.py

@@ -88,7 +88,9 @@
 # exists before adding the channel.
 mkdir -p {self.container_staging}/linux-64
 mkdir -p {self.container_staging}/noarch
+mkdir -p {self.container_package_cache}
 conda config --add channels file://{self.container_staging}  > /dev/null 2>&1
+export CONDA_PKGS_DIRS={self.container_package_cache}
 
 # The actual building...
 # we explicitly point to the meta.yaml, in order to keep
@@ -192,6 +194,7 @@ def __init__(
         tag='tmp-bioconda-builder',
         container_recipe='/opt/recipe',
         container_staging="/opt/host-conda-bld",
+        container_package_cache="/opt/anaconda-pkg-cache",
         requirements=None,
         build_script_template=BUILD_SCRIPT_TEMPLATE,
         dockerfile_template=DOCKERFILE_TEMPLATE,
@@ -219,6 +222,9 @@ def __init__(
             Upon successful building container-built packages will be copied
             over. Mounted as read-write.
 
+        container_package_cache: str
+            If you are using package caches put them here
+
         requirements : None or str
             Path to a "requirements.txt" file which will be installed with
             conda in a newly-created container. If None, then use the default
@@ -322,6 +328,8 @@ def __init__(
 
         self.container_recipe = container_recipe
         self.container_staging = container_staging
+        ##TODO Clean this up - should get it from the environmental variable
+        self.container_package_cache = container_package_cache
         self.host_conda_bld = get_host_conda_bld()
 
         if use_host_conda_bld:
@@ -450,14 +458,20 @@ def build_recipe(self, recipe_dir, build_args, env, pkg, noarch=False):
             env_list.append('-e')
             env_list.append('{0}={1}'.format(k, v))
 
+        volume_mounts = [
+            '-v', '{0}:/opt/build_script.bash'.format(build_script),
+            '-v', '{0}:{1}'.format(self.pkg_dir, self.container_staging),
+            '-v', '{0}:{1}'.format(recipe_dir, self.container_recipe),
+        ]
+
+        if os.environ.get('CONDA_PKGS_DIRS'):
+            volume_mounts = volume_mounts + ['-v', '{0}:{1}'.format(os.environ.get('CONDA_PKGS_DIRS'), self.container_package_cache)]
+
         cmd = [
             'docker', 'run',
             '--net', 'host',
             '--rm',
-            '-v', '{0}:/opt/build_script.bash'.format(build_script),
-            '-v', '{0}:{1}'.format(self.pkg_dir, self.container_staging),
-            '-v', '{0}:{1}'.format(recipe_dir, self.container_recipe),
-        ] + env_list + [
+        ] + volume_mounts + env_list + [
             self.tag,
             '/bin/bash', '/opt/build_script.bash',
         ]

bioconda_utils/pkg_test.py

@@ -79,7 +79,8 @@ def test_package(
     name_override=None,
     channels=["conda-forge", "defaults"],
     mulled_args="",
-    base_image=None
+    base_image=None,
+    mulled_upload_target='biocontainers'
 ):
     """
     Tests a built package in a minimal docker container.
@@ -104,6 +105,9 @@ def test_package(
     base_image : None | str
         Specify custom base image. Busybox is used in the default case.
 
+    mulled_upload_target : biocontainers | str
+        Namespace for docker container
+
     """
 
     assert path.endswith('.tar.bz2'), "Unrecognized path {0}".format(path)
@@ -130,9 +134,10 @@ def test_package(
         'mulled-build',
         'build-and-test',
         spec,
-        '-n', 'biocontainers',
+        '-n', mulled_upload_target,
         '--test', tests
     ]
+    logger.debug('Cmd to run: %s' % cmd)
     if name_override:
         cmd += ['--name-override', name_override]
     cmd += channel_args