Merge pull request #1188 from consideRatio/pr/ci-speedup

ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min
jupyterhub · Oct 18, 2022 · 380f817 · 380f817
2 parents d7be04e + 1e4bc50
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diff --git a/docs/source/config_files.rst b/docs/source/config_files.rst
@@ -144,9 +144,10 @@ To install your repository like an R package, you may include a
 ``DESCRIPTION`` file. repo2docker installs the package and dependencies
 from the ``DESCRIPTION`` by running ``devtools::install_local(getwd())``.
 
-You also need to have a ``runtime.txt`` file that is formatted as
-``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot of MRAN that will be
-used for your R installation.
+You can also have have a ``runtime.txt`` file that is formatted as
+``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot of CRAN that will be used
+for your R installation. If ``runtime.txt`` isn't provided in this case, a
+recent date will be used.
 
 
 .. _postBuild:

diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py
@@ -50,6 +50,16 @@ def julia_version(self):
             compat = project_toml["compat"]["julia"]
         except:
             # Default version which needs to be manually updated with new major.minor releases
+            #
+            # NOTE: Updates to the default version should go hand in hand with
+            #       updates to tests/julia/project/verify where is intent to
+            #       test the version.
+            #
+            # FIXME: When compat = "1.6" is set below and passed to
+            #        find_semver_match, we get 1.8.2 as of 2022-10-09. We should
+            #        clarify the desired behavior and have a unit test of
+            #        find_semver_match to validate it.
+            #
             compat = "1.6"
 
         match = find_semver_match(compat, self.all_julias)

diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py
@@ -79,7 +79,7 @@ def r_version(self):
         #
         # NOTE: When updating this version, also update
         #       - tests/unit/test_r.py -> test_version_specification
-        #       - tests/r/simple/verify
+        #       - tests/r/r-rspm-apt/verify
         #
         r_version = version_map["4.2"]
 

diff --git a/tests/conda/README.md b/tests/conda/README.md
@@ -0,0 +1,63 @@
+# Overview of tests for the conda buildpack
+
+## Tested configuration files
+
+- [`.binder/`](https://repo2docker.readthedocs.io/en/latest/usage.html#where-to-put-configuration-files)
+- [`requirements.txt`](https://repo2docker.readthedocs.io/en/latest/config_files.html#requirements-txt-install-a-python-environment)
+- [`postBuild](https://repo2docker.readthedocs.io/en/latest/config_files.html#postbuild-run-code-after-installing-the-environment)
+
+## Tested repo2docker command line flags
+
+- [`--target-repo-dir`](https://repo2docker.readthedocs.io/en/latest/usage.html#cmdoption-jupyter-repo2docker-target-repo-dir)
+
+### 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.
+
+### 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.
+
+### py-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.
+
+### 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.
+
+  `--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`.
diff --git a/tests/conda/binder-dir/Dockerfile b/tests/conda/binder-dir/Dockerfile
diff --git a/tests/conda/binder-dir/environment.yml b/tests/conda/binder-dir/environment.yml
diff --git a/tests/conda/channel-dep/environment.yml b/tests/conda/channel-dep/environment.yml
diff --git a/tests/conda/channel-dep/verify b/tests/conda/channel-dep/verify
diff --git a/tests/conda/default-env/postBuild b/tests/conda/default-env/postBuild
diff --git a/tests/conda/default-env/verify b/tests/conda/default-env/verify
diff --git a/tests/conda/default-env/verify.py b/tests/conda/default-env/verify.py
diff --git a/tests/conda/simple/environment.yml → ...conda/py-r-postbuild-file/environment.yml b/tests/conda/simple/environment.yml → ...conda/py-r-postbuild-file/environment.yml
@@ -1,3 +1,4 @@
 dependencies:
-  - numpy
   - pytest
+  - r-base
+  - r-digest
diff --git a/tests/conda/py-r-postbuild-file/postBuild b/tests/conda/py-r-postbuild-file/postBuild
@@ -0,0 +1,2 @@
+#!/bin/bash
+pip install there
diff --git a/tests/conda/r-unspecified/verify → tests/conda/py-r-postbuild-file/verify b/tests/conda/r-unspecified/verify → tests/conda/py-r-postbuild-file/verify
@@ -2,6 +2,11 @@
 
 jupyter serverextension list 2>&1 | grep jupyter_server_proxy
 jupyter nbextension list 2>&1 | grep jupyter_server_proxy
-R -e "library('ggplot2')"
-# Fail if version is not at least 4.1
-R -e 'if (!(version$major == "4" && as.double(version$minor) >= 1)) quit("yes", 1)'
+
+R -e "library('digest')"
+
+# Fail if version is not at least 4.2
+R --version
+R -e 'if (!(version$major == "4" && as.double(version$minor) >= 2)) quit("yes", 1)'
+
+pytest --verbose --color=yes ./verify.py
diff --git a/tests/conda/simple/verify.py → tests/conda/py-r-postbuild-file/verify.py b/tests/conda/simple/verify.py → tests/conda/py-r-postbuild-file/verify.py
@@ -4,11 +4,13 @@
 
 
 def test_sys_version():
+    """The default python version should be 3.7"""
     assert sys.version_info[:2] == (3, 7)
 
 
-def test_numpy():
-    import numpy
+def test_there():
+    """there is to be installed via postBuild"""
+    import there
 
 
 def test_conda_activated():

diff --git a/tests/conda/simple-py2/environment.yml → tests/conda/py2/environment.yml b/tests/conda/simple-py2/environment.yml → tests/conda/py2/environment.yml
diff --git a/tests/conda/simple-py2/verify → tests/conda/py2/verify b/tests/conda/simple-py2/verify → tests/conda/py2/verify
diff --git a/tests/conda/py310-requirements-file/environment.yml b/tests/conda/py310-requirements-file/environment.yml
@@ -0,0 +1,6 @@
+dependencies:
+  - python=3.10
+  - numpy
+  - pip
+  - pip:
+      - simplejson
diff --git a/tests/conda/requirements/requirements.txt → .../py310-requirements-file/requirements.txt b/tests/conda/requirements/requirements.txt → .../py310-requirements-file/requirements.txt
diff --git a/tests/conda/requirements/verify → tests/conda/py310-requirements-file/verify b/tests/conda/requirements/verify → tests/conda/py310-requirements-file/verify
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import sys
 
-assert sys.version_info[:2] == (3, 7), sys.version
+assert sys.version_info[:2] == (3, 10), sys.version
 
 import numpy
 

diff --git a/...s/conda/binder-dir/binder/environment.yml → ...a/py35-binder-dir/.binder/environment.yml b/...s/conda/binder-dir/binder/environment.yml → ...a/py35-binder-dir/.binder/environment.yml
diff --git a/tests/conda/py35-binder-dir/Dockerfile b/tests/conda/py35-binder-dir/Dockerfile
@@ -0,0 +1,2 @@
+# This file should be ignored because there's a dedicated binder folder
+FROM doesntmatter
diff --git a/tests/conda/py35-binder-dir/environment.yml b/tests/conda/py35-binder-dir/environment.yml
@@ -0,0 +1,4 @@
+# This file should be ignored as we have a dedicated binder folder.
+dependencies:
+  - thiswontwork
+  invalid
diff --git a/tests/conda/binder-dir/verify → tests/conda/py35-binder-dir/verify b/tests/conda/binder-dir/verify → tests/conda/py35-binder-dir/verify
diff --git a/tests/conda/py37/environment.yml b/tests/conda/py37/environment.yml
diff --git a/tests/conda/py37/verify b/tests/conda/py37/verify
diff --git a/tests/conda/py38/environment.yml b/tests/conda/py38/environment.yml
diff --git a/tests/conda/py38/verify b/tests/conda/py38/verify
diff --git a/tests/conda/r-unspecified/environment.yml b/tests/conda/r-unspecified/environment.yml
diff --git a/tests/conda/r3.6/environment.yml → ...r3.6-target-repo-dir-flag/environment.yml b/tests/conda/r3.6/environment.yml → ...r3.6-target-repo-dir-flag/environment.yml
@@ -1,3 +1,3 @@
 dependencies:
   - r-base=3.6
-  - r-testthat
+  - r-digest
diff --git a/tests/conda/r3.6-target-repo-dir-flag/test-extra-args.yaml b/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 repo2docker's command line flags.
+#
+- --target-repo-dir=/srv/repo
diff --git a/tests/conda/r3.6/verify → tests/conda/r3.6-target-repo-dir-flag/verify b/tests/conda/r3.6/verify → tests/conda/r3.6-target-repo-dir-flag/verify
@@ -2,6 +2,11 @@
 
 jupyter serverextension list 2>&1 | grep jupyter_server_proxy
 jupyter nbextension list 2>&1 | grep jupyter_server_proxy
-R -e "library('testthat')"
-# Fail if version is not 3.6
+
+R -e "library('digest')"
+
+# 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)'
+
+./verify.py
diff --git a/tests/conda/repo-path/verify → ...conda/r3.6-target-repo-dir-flag/verify.py b/tests/conda/repo-path/verify → ...conda/r3.6-target-repo-dir-flag/verify.py
@@ -10,11 +10,8 @@
 assert sys.executable.startswith("/srv/conda/"), sys.executable
 
 # Repo should be in /srv/repo
-assert os.path.exists("/srv/repo/verify")
-assert os.path.abspath(__file__) == "/srv/repo/verify"
+assert os.path.exists("/srv/repo/verify.py")
+assert os.path.abspath(__file__) == "/srv/repo/verify.py"
 
 # Repo should be writable
 assert os.access("/srv/repo", os.W_OK)
-
-# We should be able to import the package in environment.yml
-import numpy
diff --git a/tests/conda/r4.0/environment.yml b/tests/conda/r4.0/environment.yml
diff --git a/tests/conda/r4.0/verify b/tests/conda/r4.0/verify
diff --git a/tests/conda/r4.1/environment.yml b/tests/conda/r4.1/environment.yml
diff --git a/tests/conda/r4.1/verify b/tests/conda/r4.1/verify
diff --git a/tests/conda/repo-path/README.rst b/tests/conda/repo-path/README.rst
diff --git a/tests/conda/repo-path/environment.yml b/tests/conda/repo-path/environment.yml
diff --git a/tests/conda/repo-path/extra-args.yaml b/tests/conda/repo-path/extra-args.yaml
diff --git a/tests/conda/requirements/README.rst b/tests/conda/requirements/README.rst
diff --git a/tests/conda/requirements/environment.yml b/tests/conda/requirements/environment.yml
diff --git a/tests/conda/simple-py2/README.rst b/tests/conda/simple-py2/README.rst
diff --git a/tests/conda/simple/README.rst b/tests/conda/simple/README.rst
diff --git a/tests/conda/simple/verify b/tests/conda/simple/verify
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -198,7 +198,7 @@ def collect(self):
         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)

diff --git a/tests/julia/README.md b/tests/julia/README.md
@@ -0,0 +1,38 @@
+# Overview of tests for the julia buildpack
+
+## Tested configuration files
+
+- [`Project.toml`](https://repo2docker.readthedocs.io/en/latest/config_files.html#project-toml-install-a-julia-environment)
+- [`REQUIRE`](https://repo2docker.readthedocs.io/en/latest/config_files.html#require-install-a-julia-environment-legacy)
+- [`requirements.txt`](https://repo2docker.readthedocs.io/en/latest/config_files.html#requirements-txt-install-a-python-environment)
+
+## Test folders
+
+### project
+
+- Tests use of a `Project.toml` file for Julia, using the repo2docker default
+  version of Julia as specified in `julia_project.py`.
+
+### project-1.0.2
+
+- Tests use of a `Project.toml` file for Julia, using a version of Julia
+  specified via `julia = "=1.0.2"` in `Project.toml`'s `[compat]` section.
+
+### require
+
+- Tests use of a `REQUIRE` file for Julia, using the repo2docker default version
+  of Julia as specified in `julia_require.py`. Note that this is default version
+  is currently 0.6.4!
+
+- Starting with Julia v0.7 and up, the package manager has changed, so this
+  tests that the Julia version below that can be installed correctly as well.
+
+### require-1-requirements-file
+
+- Tests use of a `REQUIRE` file for Julia, using a major version version
+  specification. Note that this major version specification is currently
+  resolving to a pinned minor and patch version as declared in
+  `julia_require.py`.
+
+- Test use of a `requirements.txt` file, where it is expected to be respected
+  alongside the `REQUIRE` file.