Merge pull request #942 from yuvipanda/conda-channels

 Add the ability to define conda channels in plugins via `tljh_extra_user_conda_channels`

integration-tests/plugins/simplest/tljh_simplest.py

@@ -7,7 +7,14 @@
 
 @hookimpl
 def tljh_extra_user_conda_packages():
-    return ["tqdm"]
+    # tqdm installs from the conda-forge channel (https://conda-forge.org/packages/)
+    # csvtk installs from the bioconda channel (https://bioconda.github.io/conda-package_index.html)
+    return ["tqdm", "csvtk"]
+
+
+@hookimpl
+def tljh_extra_user_conda_channels():
+    return ["conda-forge", "bioconda"]
 
 
 @hookimpl

integration-tests/test_simplest_plugin.py

@@ -27,6 +27,17 @@ def test_tljh_extra_hub_pip_packages():
     subprocess.check_call([f"{HUB_ENV_PREFIX}/bin/python3", "-c", "import there"])
 
 
+def test_conda_packages():
+    """
+    Test extra user conda packages are installed from multiple channels.
+
+    - tqdm installs from the conda-forge channel (https://conda-forge.org/packages/)
+    - csvtk installs from the bioconda channel (https://bioconda.github.io/conda-package_index.html)
+    """
+    subprocess.check_call([f"{USER_ENV_PREFIX}/bin/python3", "-c", "import tqdm"])
+    subprocess.check_call([f"{USER_ENV_PREFIX}/bin/csvtk", "cat", "--help"])
+
+
 def test_tljh_extra_apt_packages():
     assert os.path.exists("/usr/games/sl")
 

tests/test_conda.py

@@ -34,6 +34,15 @@ def test_ensure_packages(prefix):
     subprocess.check_call([os.path.join(prefix, "bin", "python"), "-c", "import numpy"])
 
 
+def test_ensure_channel_packages(prefix):
+    """
+    Test installing packages in conda environment
+    """
+    conda.ensure_conda_packages(prefix, ["csvtk"], channels=("conda-forge", "bioconda"))
+    # Throws an error if this fails
+    subprocess.check_call([os.path.join(prefix, "bin", "csvtk"), "cat", "--help"])
+
+
 def test_ensure_pip_packages(prefix):
     """
     Test installing pip packages in conda environment

tljh/conda.py

@@ -99,9 +99,11 @@ def install_miniconda(installer_path, prefix):
     fix_permissions(prefix)
 
 
-def ensure_conda_packages(prefix, packages, force_reinstall=False):
+def ensure_conda_packages(
+    prefix, packages, channels=("conda-forge",), force_reinstall=False
+):
     """
-    Ensure packages (from conda-forge) are installed in the conda prefix.
+    Ensure packages (from channels) are installed in the conda prefix.
 
     Note that conda seem to update dependencies by default, so there is probably
     no need to have a update parameter exposed for this function.
@@ -118,13 +120,14 @@ def ensure_conda_packages(prefix, packages, force_reinstall=False):
         # avoids problems with RemoveError upgrading conda from old versions
         cmd += ["--force-reinstall"]
 
+    for channel in channels:
+        cmd += ["-c", channel]
+
     abspath = os.path.abspath(prefix)
 
     utils.run_subprocess(
         cmd
         + [
-            "-c",
-            "conda-forge",  # Make customizable if we ever need to
             "--prefix",
             abspath,
         ]

tljh/hooks.py

@@ -15,6 +15,13 @@ def tljh_extra_user_conda_packages():
     """
 
 
+@hookspec
+def tljh_extra_user_conda_channels():
+    """
+    Return a list of conda channels to be used during user environment installation.
+    """
+
+
 @hookspec
 def tljh_extra_user_pip_packages():
     """

tljh/installer.py

@@ -449,13 +449,18 @@ def run_plugin_actions(plugin_manager):
 
     # Install conda packages
     conda_packages = list(set(itertools.chain(*hook.tljh_extra_user_conda_packages())))
+    conda_channels = list(itertools.chain(*hook.tljh_extra_user_conda_channels()))
+    if len(conda_channels) == 0:
+        conda_channels = ("conda-forge",)
     if conda_packages:
         logger.info(
             "Installing {} user conda packages collected from plugins: {}".format(
                 len(conda_packages), " ".join(conda_packages)
             )
         )
-        conda.ensure_conda_packages(USER_ENV_PREFIX, conda_packages)
+        conda.ensure_conda_packages(
+            USER_ENV_PREFIX, conda_packages, channels=conda_channels
+        )
 
     # Install pip packages
     user_pip_packages = list(set(itertools.chain(*hook.tljh_extra_user_pip_packages())))