ci: adjust to and rename extra-args.yaml to test-extra-args.yaml

I misunderstood extra-args.yaml to be a file that was recognized by
repo2docker's CLI, but in reality it was just a file recognized by the
repo2docker test suite. Following that, I renamed this testing specific
file to test-extra-args.yaml to help others avoid making that mistake
and added comments to clarify that.

This commit also gathers the conda buildpacks separate readme files into
a single readme file.

tests/conda/README.md

@@ -0,0 +1,57 @@
+# Overview of tests for the conda buildpack
+
+## py2
+
+- Test setup of a Python 2 environment by declaring `python=2` in
+  `environment.yml`.
+
+## py35-binder-dir
+
+- Test setup of a Python 3.5 environment by declaring `python=3.5` in
+  `environment.yml`.
+
+  The reasons for testing 3.5 specifically is that it is the oldest version of
+  Python 3 supported by repo2docker's conda buildpack. See
+  `repo2docker/buildpacks/conda` for details.
+
+- Test use of a `.binder` directory, where files outside it shouldn't be
+  considered. See [this documentation](https://repo2docker.readthedocs.io/en/latest/usage.html#where-to-put-configuration-files)
+  for details.
+
+## py310-requirements-file
+
+- Test setup of a Python 3.10 environment by declaring `python=3.10` in
+  `environment.yml`.
+
+  The reasons for testing 3.10 specifically is that it is the newest version of
+  Python 3 supported by repo2docker's conda buildpack. See
+  `repo2docker/buildpacks/conda` for details.
+
+- Test use of a `requirements.txt` file, where an `environment.yml` file should
+  take precedence and the `requirements.txt` should be ignored.
+
+## r-postbuild-file
+
+- Test setup of the default Python environment by omitting `python` from
+  `environment.yml` file.
+
+- Test setup of the default R environment by specifying `r-base` in
+  `environment.yml`.
+
+- Test use of a `postBuild` file. See [this documentation](https://repo2docker.readthedocs.io/en/latest/config_files.html#postbuild-run-code-after-installing-the-environment)
+  for details.
+
+## r3.6-target-repo-dir-flag
+
+- Test setup of a R 3.6 environment by specifying `r-base=3.6` in
+  `environment.yml`.
+
+- Test use of repo2docker with the `--target-repo-dir` flag. See [this documentation](https://repo2docker.readthedocs.io/en/latest/usage.html#cmdoption-jupyter-repo2docker-target-repo-dir)
+  for details.
+
+  `--target-repo-dir` is meant to support custom paths where repositories can be
+  copied to besides `${HOME}`.
+  
+  This test makes use of the `test-extra-args.yaml` file to influence additional
+  arguments passed to `repo2docker` during the test. In this test, specify
+  `--target-repo-dir=/srv/repo`.

tests/conda/py2/README.rst

@@ -1,4 +0,0 @@
-Python 2
---------
-
-Test setup of a Python 2 environment.

tests/conda/py310-requirements-file/README.rst

@@ -1,17 +0,0 @@
-Python 3.10 (latest), and an ignored requirements file
-------------------------------------------------------
-
-The reasons for testing 3.10 specifically is that it is the latest version of
-Python 3 supported by repo2docker's conda buildpack. See
-``repo2docker/buildpacks/conda`` for details.
-
-An ``environment.yml`` file takes precedence over ``requirements.txt``.
-To install Python packages into a conda environment with pip, use the
-``pip`` key in ``environment.yml``:
-
-.. sourcecode:: yaml
-
-   dependencies:
-     - numpy
-     - pip:
-       - tornado

tests/conda/py310-requirements-file/environment.yml

@@ -1,5 +1,6 @@
 dependencies:
   - python=3.10
   - numpy
+  - pip
   - pip:
-    - simplejson
+      - simplejson

tests/conda/py35-binder-dir/README.rst

@@ -1,9 +0,0 @@
-Python 3.5, and a dedicated binder folder
------------------------------------------
-
-Test setup of Python 3.5 and the use of a dedicated binder folder that should
-make files in the root directory be ignored.
-
-The reasons for testing 3.5 specifically is that it is the oldest version of
-Python 3 supported by repo2docker's conda buildpack. See
-``repo2docker/buildpacks/conda`` for details.

tests/conda/r-postbuild/README.rst

@@ -1,6 +0,0 @@
-Default R, default Python, and a postBuild file
------------------------------------------------
-
-We test the default R and Python version set by repo2docker as used when an
-environment.yml file is provided without a ``python`` or ``r-base`` dependency
-pinned, and the use of a ``postBuild`` file.

tests/conda/r3.6-extra-args/README.rst

@@ -1,7 +0,0 @@
-R 3.6, and an extra-args.yaml file
-----------------------------------
-
-We want to support custom paths where repositories can be copied to, instead of
-${HOME}. The `extra-args.yaml` file in each dir can contain a list of arguments
-that are passed to repo2docker during the test. We copy this repo to /srv/repo
-instead of ${HOME}

tests/conda/r3.6-extra-args/extra-args.yaml

@@ -1,2 +0,0 @@
-- --target-repo-dir
-- /srv/repo

tests/conda/r3.6-target-repo-dir-flag/test-extra-args.yaml

@@ -0,0 +1,4 @@
+# This file is respected by repo2docker's test suite, but not repo2docker
+# itself. It is used solely to help us test command line flags.
+#
+- --target-repo-dir=/srv/repo

tests/conda/r3.6-target-repo-dir-flag/verify

@@ -5,7 +5,7 @@ jupyter nbextension list 2>&1 | grep jupyter_server_proxy
 
 R -e "library('digest')"
 
-# Fail if version is not 3.6
+# Fail if R version is not 3.6
 R --version
 R -e 'if (!(version$major == "3" && as.double(version$minor) >= 6 && as.double(version$minor) < 7)) quit("yes", 1)'
 

tests/conftest.py

@@ -198,7 +198,7 @@ class LocalRepo(pytest.File):
         args = ["--appendix", 'RUN echo "appendix" > /tmp/appendix']
         # If there's an extra-args.yaml file in a test dir, assume it contains
         # a yaml list with extra arguments to be passed to repo2docker
-        extra_args_path = os.path.join(self.fspath.dirname, "extra-args.yaml")
+        extra_args_path = os.path.join(self.fspath.dirname, "test-extra-args.yaml")
         if os.path.exists(extra_args_path):
             with open(extra_args_path) as f:
                 extra_args = yaml.safe_load(f)