Merge pull request #334 from bioconda/cf-prio

Use conda-forge with a higher priority than bioconda.

Author: bgruening

.circleci/setup.sh

@@ -30,8 +30,8 @@ if [[ ! -d $WORKSPACE/miniconda ]]; then
     # step 2: setup channels
 
     conda config --system --add channels defaults
-    conda config --system --add channels conda-forge
     conda config --system --add channels bioconda
+    conda config --system --add channels conda-forge
 
     # step 3: install bioconda-utils and test requirements
     conda install -y --file bioconda_utils/bioconda_utils-requirements.txt --file test-requirements.txt
@@ -40,7 +40,8 @@ if [[ ! -d $WORKSPACE/miniconda ]]; then
     conda clean -y --all
 
     # Add local channel as highest priority
-    conda index $WORKSPACE/miniconda/conda-bld/linux-64 $WORKSPACE/miniconda/conda-bld/osx-64 $WORKSPACE/miniconda/conda-bld/noarch
+    mkdir -p $WORKSPACE/miniconda/conda-bld/{noarch,linux-64,osx-64}
+    conda index $WORKSPACE/miniconda/conda-bld
     conda config --system --add channels file://$WORKSPACE/miniconda/conda-bld
 fi
 

Dockerfile

@@ -4,8 +4,8 @@ RUN mkdir -p /tmp/repo/bioconda_utils/
 COPY ./bioconda_utils/bioconda_utils-requirements.txt /tmp/repo/bioconda_utils/
 RUN export PATH="/opt/conda/bin:${PATH}" && \
     conda config --add channels defaults && \
-    conda config --add channels conda-forge && \
-    conda config --add channels bioconda
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge
 RUN export PATH="/opt/conda/bin:${PATH}" && \
     conda install --file /tmp/repo/bioconda_utils/bioconda_utils-requirements.txt && \
     conda clean -y --all

README.md

@@ -18,7 +18,7 @@ bioconda-utils, you can install requirements via conda into your root conda
 environment and then install the package:
 
 ```bash
-conda install --file bioconda_utils/bioconda_utils-requirements.txt -c bioconda -c conda-forge
+conda install --file bioconda_utils/bioconda_utils-requirements.txt -c conda-forge -c bioconda 
 python setup.py install
 ```
 

bioconda_utils/pkg_test.py

@@ -83,7 +83,7 @@ def get_image_name(path):
 def test_package(
     path,
     name_override=None,
-    channels=["conda-forge", "defaults"],
+    channels=("conda-forge", "local", "bioconda", "defaults"),
     mulled_args="",
     base_image=None,
     conda_image=MULLED_CONDA_IMAGE,
@@ -99,9 +99,9 @@ def test_package(
     name_override : str
         Passed as the --name-override argument to mulled-build
 
-    channels : None | str | list
-        The local channel of the provided package will be added automatically;
-        `channels` are channels to use in addition to the local channel.
+    channels : list
+        List of Conda channels to use. Must include an entry "local" for the
+        local build channel.
 
     mulled_args : str
         Mechanism for passing arguments to the mulled-build command. They will
@@ -127,13 +127,17 @@ def test_package(
 
     spec = get_image_name(path)
 
-    extra_channels = ['file://{0}'.format(conda_bld_dir)]
-    if channels is None:
-        channels = []
-    if isinstance(channels, str):
-        channels = [channels]
-    extra_channels.extend(channels)
-    channel_args = ['--extra-channels', ','.join(extra_channels)]
+    if "local" not in channels:
+        raise ValueError('"local" must be in channel list')
+
+    channel, *extra_channels = [
+        'file://{0}'.format(conda_bld_dir) if channel == 'local' else 'channel'
+        for channel in channels
+    ]
+    # '--channel' currently defaults to 'bioconda' in mulled-build and is
+    # prepended to all remaining channels. To prevent this, i.e., to give
+    # 'conda-forge' a higher priority, we use '--channel' explicitly here.
+    channel_args = ['--channel', channel, '--extra-channels', ','.join(extra_channels)]
 
     tests = get_tests(path)
     logger.debug('Tests to run: %s', tests)

docs/source/cb3.rst

@@ -156,7 +156,7 @@ After:
 
 .. warning::
 
-    These compilers are only available in the ``anaconda`` channel. Until now
+    These compilers are only available in the ``defaults`` channel. Until now
     we have not had this channel as a dependency, so be sure to add the channel
     when setting up bioconda (see :ref:`set-up-channels`).
 

docs/source/faqs.rst

@@ -108,7 +108,7 @@ the `broken` label, i.e.,
 
 .. code-block:: bash
 
-    conda install -c bioconda -c conda-forge -c defaults -c bioconda/label/broken my-package=<broken-version>
+    conda install -c conda-forge -c bioconda -c defaults -c bioconda/label/broken my-package=<broken-version>
 
 
 .. _circlecimacos:

docs/source/guidelines.rst

@@ -13,7 +13,7 @@ bioconda recipe checklist
 - Adequate tests included (:ref:`details <tests>`)
 - Files created by the recipe follow the FSH (:ref:`details <fsh-section>`)
 - License allows redistribution and license is indicated in ``meta.yaml``
-- Package does not already exist in the `defaults`, `r`, or `conda-forge`
+- Package does not already exist in the `defaults` or `conda-forge`
   channels with some exceptions (:ref:`details <channel-exceptions>`)
 - Package is appropriate for bioconda (:ref:`details <appropriate-for-bioconda>`)
 - If the recipe installs custom wrapper scripts, usage notes should be added to
@@ -112,7 +112,7 @@ consider opening a pull request with `conda-forge
 <https://conda-forge.github.io/#add_recipe>`_ which hosts general packages.
 
 The exception to this is with R packages. We are still coordinating with
-anaconda and conda-forge about the best place to keep general R packages. In
+Anaconda and conda-forge about the best place to keep general R packages. In
 the meantime, R packages that are not specific to bioinformatics and that
 aren't already in the `conda-forge` channel can be added to bioconda.
 

docs/source/index.rst

@@ -80,21 +80,18 @@ package. The Python 3 version is recommended.
 
 After installing conda you will need to add the bioconda channel as well as the
 other channels bioconda depends on. **It is important to add them in this
-order** so that the priority is set correctly (that is, bioconda is highest
+order** so that the priority is set correctly (that is, conda-forge is highest
 priority).
 
 The `conda-forge` channel contains many general-purpose packages not already
-found in the `defaults` channel. The `r` channel is only included due to
-backward compatibility.  It is not mandatory, but without the `r` channel
-packages compiled against R 3.3.1 might not work.
+found in the `defaults` channel.
 
 
 ::
 
     conda config --add channels defaults
-    conda config --add channels conda-forge
     conda config --add channels bioconda
-
+    conda config --add channels conda-forge
 
 3. Install packages
 -------------------

test/test_bioconductor_skeleton.py

@@ -6,7 +6,7 @@
 
 
 config = {
-    'channels': ['bioconda', 'conda-forge', 'defaults']
+    'channels': ['conda-forge', 'bioconda', 'defaults']
 }
 
 
@@ -58,7 +58,7 @@ def test_bioc_write_recipe_no_skipping(tmpdir):
 
 def test_meta_contents(tmpdir):
     config = {
-        'channels': ['bioconda', 'conda-forge', 'defaults']
+        'channels': ['conda-forge', 'bioconda', 'defaults']
     }
     bioconductor_skeleton.write_recipe(
         'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False)