narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

Improve handling of pip arguments when detecting local dependencies

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -466,7 +466,15 @@ def is_local_pip_requirement(line): if line.startswith(("-r", "-c")): # local -r or -c references break isolation return True - # strip off `-e, etc.` + if line.startswith(("--requirement", "--constraint")): + # as above but flags are spelt out + return True + # strip off things like `--editable=`. Long form arguments require a = + if line.startswith("--"): + line = line.split("=", 1)[1] + # strip off short form arguments like `-e`. Short form arguments can be + # followed by a space `-e foo` or use `-e=foo`. The latter is not handled + # here. We can deal with it when we see someone using it. if line.startswith("-"): line = line.split(None, 1)[1] if "file://" in line: MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -135,6 +135,7 @@ def test_open_guess_encoding(): [ ("-r requirements.txt", True), ("-e .", True), + ("--editable=.", True), ("file://subdir", True), ("file://./subdir", True), ("git://github.com/jupyter/repo2docker", False),

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Add reported failing spec

MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -136,6 +136,10 @@ def test_open_guess_encoding(): ("-r requirements.txt", True), ("-e .", True), ("--editable=.", True), + ( + "--editable=git+https://github.com/popgensims/stdpopsim.git#egg=stdpopsim-master", + False, + ), ("file://subdir", True), ("file://./subdir", True), ("git://github.com/jupyter/repo2docker", False),

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Update server proxy and rsession proxy Both haven't been updated in a long time (~1yr) so we should refresh them. This brings both to the latest commit in their repos.

MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -55,8 +55,8 @@ def rstudio_base_scripts(): "${NB_USER}", # Install nbrsessionproxy r""" - pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \ - pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \ + pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/00be53dfed8ab5a0baaf8332e3fc6bd44dc5bf1a.zip && \ + pip install --no-cache-dir https://github.com/jupyterhub/jupyter-rsession-proxy/archive/d5efed5455870556fc414f30871d0feca675a4b4.zip && \ jupyter serverextension enable jupyter_server_proxy --sys-prefix && \ jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \ jupyter nbextension enable --py jupyter_server_proxy --sys-prefix

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Update repo2docker/buildpacks/_r_base.py

MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -55,7 +55,7 @@ def rstudio_base_scripts(): "${NB_USER}", # Install nbrsessionproxy r""" - pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/00be53dfed8ab5a0baaf8332e3fc6bd44dc5bf1a.zip && \ + pip install --no-cache-dir jupyter-server-proxy==1.3.2 && \ pip install --no-cache-dir https://github.com/jupyterhub/jupyter-rsession-proxy/archive/d5efed5455870556fc414f30871d0feca675a4b4.zip && \ jupyter serverextension enable jupyter_server_proxy --sys-prefix && \ jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \

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[docs] fix grammatical error in section title

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -56,7 +56,7 @@ file. We support R versions 3.4, 3.5 and 3.6. -Why is my repository is failing to build with ``ResolvePackageNotFound`` ? +Why is my repository failing to build with ``ResolvePackageNotFound`` ? -------------------------------------------------------------------------- If you used ``conda env export`` to generate your ``environment.yml`` it will

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Placeholder for work to come.

MODIFY repo2docker/app.py repo2docker/app.py @@ -560,6 +560,8 @@ class Repo2Docker(Application): "mode": "rw", } + # self.environment needs to be modified to match the semantics + # of docker's --env option run_kwargs = dict( publish_all_ports=self.all_ports, ports=ports,

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Work around a Julia bug

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -136,7 +136,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): "${NB_USER}", r""" JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && \ - julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); pkg"precompile"' + julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"' """, ) ]

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Add failing test for bare env argument value

MODIFY tests/unit/test_env.py tests/unit/test_env.py @@ -15,6 +15,7 @@ def test_env(): ts = str(time.time()) with tempfile.TemporaryDirectory() as tmpdir: username = getuser() + os.environ["SPAM"] = "eggs" subprocess.check_call( [ "repo2docker", @@ -24,11 +25,13 @@ def test_env(): "FOO={}".format(ts), "--env", "BAR=baz", + "--env", + "SPAM", "--", tmpdir, "/bin/bash", "-c", - "echo -n $FOO > ts && echo -n $BAR > bar", + "echo -n $FOO > ts && echo -n $BAR > bar && echo -n $SPAM > eggs", ] ) @@ -36,3 +39,5 @@ def test_env(): assert f.read().strip() == ts with open(os.path.join(tmpdir, "bar")) as f: assert f.read().strip() == "baz" + with open(os.path.join(tmpdir, "eggs")) as f: + assert f.read().strip() == "eggs"

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Refactor to eliminate need for volume mount This change allows, imo, the test to be clearer, and should also speed up the test.

MODIFY tests/unit/test_env.py tests/unit/test_env.py @@ -16,11 +16,9 @@ def test_env(): with tempfile.TemporaryDirectory() as tmpdir: username = getuser() os.environ["SPAM"] = "eggs" - subprocess.check_call( + result = subprocess.run( [ "repo2docker", - "-v", - "{}:/home/{}".format(tmpdir, username), "-e", "FOO={}".format(ts), "--env", @@ -31,13 +29,18 @@ def test_env(): tmpdir, "/bin/bash", "-c", - "echo -n $FOO > ts && echo -n $BAR > bar && echo -n $SPAM > eggs", - ] + # Docker exports all passed env variables, so we can + # just look at that output + "export", + ], + universal_newlines=True, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, ) - - with open(os.path.join(tmpdir, "ts")) as f: - assert f.read().strip() == ts - with open(os.path.join(tmpdir, "bar")) as f: - assert f.read().strip() == "baz" - with open(os.path.join(tmpdir, "eggs")) as f: - assert f.read().strip() == "eggs" + assert result.returncode == 0 + # all docker output is returned by repo2docker on stderr + # extract just the declare for better failure message formatting + declares = [x for x in result.stderr.split("\n") if x.startswith("declare")] + assert 'declare -x FOO="{}"'.format(ts) in declares + assert 'declare -x BAR="baz"' in declares + assert 'declare -x SPAM="eggs"' in declares

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env handling now consistent with Docker Added a custom action handler for '-e' and '--env' so that the 'environment' variable passed to docker reflects how docker would have processed the same args

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -39,6 +39,27 @@ def validate_image_name(image_name): return image_name +# See https://github.com/jupyter/repo2docker/issues/871 for reason +class MimicDockerEnvHandling(argparse.Action): + def __call__(self, parser, namespace, values, option_string=None): + # There are 3 cases: + # key=value pass as is + # key= pass as is + # key pass using current value, or don't pass + if "=" not in values: + try: + value_to_append = "{}={}".format(values, os.environ[values]) + except KeyError: + # no local def, so don't pass + return + else: + value_to_append = values + + # destination variable is initially defined as an empty list, so + # no special casing of first time is needed. + getattr(namespace, self.dest).append(value_to_append) + + def get_argparser(): """Get arguments that may be used by repo2docker""" argparser = argparse.ArgumentParser( @@ -161,12 +182,11 @@ def get_argparser(): # Process the environment options the same way that docker does, as # they are passed directly to docker as the environment to use. This # requires a custom action for argparse. - # see https://docs.docker.com/engine/reference/commandline/run/#set-environment-variables--e---env---env-file argparser.add_argument( "--env", "-e", dest="environment", - action="append", + action=MimicDockerEnvHandling, help="Environment variables to define at container run time", default=[], )

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pypi jupyter-offlinenotebook==0.1.0

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -46,7 +46,7 @@ conda env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml # Install jupyter-offline-notebook to allow users to download notebooks # after the server connection has been lost # This will install and enable the extension for jupyter notebook -${NB_PYTHON_PREFIX}/bin/python -m pip install https://github.com/manics/jupyter-offlinenotebook/archive/7ba3520.zip +${NB_PYTHON_PREFIX}/bin/python -m pip install jupyter-offlinenotebook==0.1.0 # and this installs it for lab. Keep going if the lab version is incompatible # with the extension ${NB_PYTHON_PREFIX}/bin/jupyter labextension install jupyter-offlinenotebook || true

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Fix test_env.py This works around an issue where the temp directory can not be added to Docker. In this case, the directory is immediately deleted, and does not occupy significant disk space. There should be no impact to the move.

MODIFY tests/unit/test_env.py tests/unit/test_env.py @@ -13,7 +13,11 @@ def test_env(): Validate that you can define environment variables """ ts = str(time.time()) - with tempfile.TemporaryDirectory() as tmpdir: + # There appear to be some odd combinations of default dir that do + # not work on macOS Catalina with Docker CE 2.2.0.5, so use + # the current dir -- it'll be deleted immediately + + with tempfile.TemporaryDirectory(dir=os.path.abspath(os.curdir)) as tmpdir: username = getuser() subprocess.check_call( [

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chmod start script from repo2docker-entrypoint

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint # we use a login shell to get a fully configured shell environment # (e.g. sourcing /etc/profile.d, ~/.bashrc, and friends) if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then + chmod u+x "$R2D_ENTRYPOINT" exec "$R2D_ENTRYPOINT" "$@" else exec "$@"

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Only chmod u+x if not already executable, in case user is not owner but file is already g/o+x

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint # we use a login shell to get a fully configured shell environment # (e.g. sourcing /etc/profile.d, ~/.bashrc, and friends) if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then + if [[ ! -x "$R2D_ENTRYPOINT" ]]; then chmod u+x "$R2D_ENTRYPOINT" + fi exec "$R2D_ENTRYPOINT" "$@" else exec "$@"

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failing docker tests locally on macOS (case 2) Fixes

MODIFY docs/source/contributing/tasks.md docs/source/contributing/tasks.md @@ -23,6 +23,16 @@ If you want to run a specific test, you can do so with: py.test -s tests/<path-to-test> ``` +### Troubleshooting Tests + +Some of the tests have non-python requirements for your development machine. They are: + +- `git-lfs` must be installed ([instructions](https://github.com/git-lfs/git-lfs)). It need not be activated -- there is no need to run the `git lfs install` command. It just needs to be available to the test suite. + - If your test failure messages include "`git-lfs filter-process: git-lfs: command not found`", this step should address the problem. + +- Minimum Docker Image size of 128GB is required. If you are not running docker on a linux OS, you may need to expand the runtime image size for your installation. See Docker's instructions for [macOS](https://docs.docker.com/docker-for-mac/space/) or [Windows 10](https://docs.docker.com/docker-for-windows/#resources) for more information. + - If your test failure messages include "`No space left on device: '/home/...`", this step should address the problem. + ## Update and Freeze BuildPack Dependencies This section covers the process by which repo2docker defines and updates the

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Bump version of irkernel for R 4.0

MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -17,7 +17,7 @@ SHINY_CHECKSUM = "9aeef6613e7f58f21c97a4600921340e" DEVTOOLS_VERSION = "2018-02-01" # IRKernel version - specified as a tag in the IRKernel repository -IRKERNEL_VERSION = "1.0.2" +IRKERNEL_VERSION = "1.1" def rstudio_base_scripts():

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Fix RShiny proxy The Shiny proxy was split out of the rstudio proxy package. This meant that RStudio sessions were still being proxied but Shiny sessions not.

MODIFY repo2docker/buildpacks/_r_base.py repo2docker/buildpacks/_r_base.py @@ -55,8 +55,9 @@ def rstudio_base_scripts(): "${NB_USER}", # Install nbrsessionproxy r""" - pip install --no-cache-dir jupyter-server-proxy==1.3.2 && \ + pip install --no-cache-dir jupyter-server-proxy==1.4.0 && \ pip install --no-cache-dir https://github.com/jupyterhub/jupyter-rsession-proxy/archive/d5efed5455870556fc414f30871d0feca675a4b4.zip && \ + pip install --no-cache-dir https://github.com/ryanlovett/jupyter-shiny-proxy/archive/47557dc47e2aeeab490eb5f3eeae414cdde4a6a9.zip && \ jupyter serverextension enable jupyter_server_proxy --sys-prefix && \ jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \ jupyter nbextension enable --py jupyter_server_proxy --sys-prefix

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Fix logo display in Sphinx docs

MODIFY docs/source/_static/custom.css docs/source/_static/custom.css img.logo { - width:100% + max-width:90%; + height: auto; } div.body p.caption { @@ -9,3 +10,11 @@ div.body p.caption { h2 a.toc-backref { text-decoration: none; } + + +.navbar-brand{ + display: flex; + justify-content:center; + align-items:center; + overflow:hidden +} \ No newline at end of file

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Update config_files.rst See Issue

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -142,7 +142,7 @@ We use ``apt.txt``, for example, to install LaTeX in our 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_git(".")``. +from the ``DESCRIPTION`` by running ``devtools::install_git(".")``. 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

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Python 2.7 wcwidth==0.1.9 Later versions of wcwidth require `backports.functools-lru-cache>=1.2.1; python_version < "3.2"` but the conda-forge wcwidth package was automatically bumped without this new requirement.

MODIFY repo2docker/buildpacks/conda/environment.py-2.7.frozen.yml repo2docker/buildpacks/conda/environment.py-2.7.frozen.yml # AUTO GENERATED FROM environment.py-2.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2020-06-02 18:05:28 UTC +# Frozen on 2020-06-03 20:30:54 UTC name: r2d channels: - conda-forge @@ -52,7 +52,7 @@ dependencies: - tk=8.6.10=hed695b0_0 - tornado=5.1.1=py27h14c3975_1000 - traitlets=4.3.3=py27h8c360ce_1 - - wcwidth=0.2.3=pyh9f0ad1d_0 + - wcwidth=0.1.9=pyh9f0ad1d_0 - wheel=0.34.2=py_1 - zeromq=4.3.2=he1b5a44_2 - zlib=1.2.11=h516909a_1006 MODIFY repo2docker/buildpacks/conda/environment.py-2.7.yml repo2docker/buildpacks/conda/environment.py-2.7.yml dependencies: - python=2.7.* - ipykernel==4.8.2 +- wcwidth==0.1.9

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Fix repo2docker logo

MODIFY docs/source/_static/custom.css docs/source/_static/custom.css img.logo { - max-width:90%; - height: auto; + max-width:100%; + height: 45px; } div.body p.caption { @@ -16,5 +16,5 @@ h2 a.toc-backref { display: flex; justify-content:center; align-items:center; - overflow:hidden + overflow:hidden; } \ No newline at end of file

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Add basic gitpod config Trying out gitpod.io to see if we can use it as a simple way to get people a working dev environment to work on the documentation.

ADD .gitpod.yml +tasks: + - init: | + pip3 install -r docs/doc-requirements.txt + pip3 install -e. + command: | + cd docs && make html && cd build/html && python3 -m http.server 8080 + name: Sphinx preview +ports: +- port: 8080

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Add sphinx-autobuild to gitpod setup

MODIFY .gitpod.yml .gitpod.yml tasks: - init: | + pip3 install sphinx-autobuild pip3 install -r docs/doc-requirements.txt pip3 install -e. command: | - cd docs && make html && cd build/html && python3 -m http.server 8080 + sphinx-autobuild docs/source/ docs/build/html/ name: Sphinx preview ports: -- port: 8080 +- port: 8000

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Use new minimum version of pytest pytest-cov requires pytest>=4.6 so we explicitly list that as a dev dependency.

MODIFY Pipfile Pipfile # update these accordingly [dev-packages] -pytest=">=3.6" +pytest=">=4.6" wheel="*" pytest-cov="*" PyYAML = "*" MODIFY dev-requirements.txt dev-requirements.txt # Note that there is also a Pipfile for this project if you are updating this # file do not forget to update the Pipfile accordingly pyyaml -pytest>=3.6 +pytest>=4.6 wheel pytest-cov pre-commit

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doc: environment.yml installs a conda env, not only python

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -22,8 +22,8 @@ can be found on this page (and to the right). .. _environment.yml: -``environment.yml`` - Install a Python environment -================================================== +``environment.yml`` - Install a conda environment +================================================= ``environment.yml`` is the standard configuration file used by `conda <https://conda.io>`_ that lets you install any kind of package,

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merge similar test cases and use equal instead of in

MODIFY tests/unit/test_binder_dir.py tests/unit/test_binder_dir.py @@ -5,22 +5,17 @@ import pytest from repo2docker import buildpacks -@pytest.mark.parametrize("binder_dir", [".binder", "binder"]) -def test_binder_dir_property(tmpdir, binder_dir): +@pytest.mark.parametrize("binder_dir", ["binder", ".binder", ""]) +def test_binder_dir(tmpdir, binder_dir): tmpdir.chdir() + if binder_dir: os.mkdir(binder_dir) bp = buildpacks.BuildPack() - assert binder_dir in bp.binder_dir + assert binder_dir == bp.binder_dir assert bp.binder_path("foo.yaml") == os.path.join(binder_dir, "foo.yaml") -def test_root_binder_dir(tmpdir): - tmpdir.chdir() - bp = buildpacks.BuildPack() - assert bp.binder_dir == "" - - def test_exclusive_binder_dir(tmpdir): tmpdir.chdir() os.mkdir("./binder")

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Disable stencila-r CI test jobs

MODIFY .travis.yml .travis.yml @@ -58,7 +58,6 @@ env: - REPO_TYPE=conda - REPO_TYPE=pipfile - REPO_TYPE=venv - - REPO_TYPE=stencila-r - REPO_TYPE=stencila-py - REPO_TYPE=julia - REPO_TYPE=r MODIFY azure-pipelines.yml azure-pipelines.yml @@ -18,9 +18,6 @@ strategy: venv: REPO_TYPE: 'venv' python_version: '3.6' - stencila_r: - REPO_TYPE: 'stencila-r' - python_version: '3.6' stencila_py: REPO_TYPE: 'stencila-py' python_version: '3.6'

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address travis lint warnings also to poke azure pipelines

MODIFY .travis.yml .travis.yml dist: xenial +os: linux language: python -sudo: required cache: pip services: - docker @@ -37,7 +37,7 @@ after_failure: deploy: provider: pypi - user: mybinderteam + username: mybinderteam distributions: sdist bdist_wheel on: tags: true

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set git env in workflows

MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -13,7 +13,11 @@ on: - pull_request # Global environment variables -env: {} +env: + GIT_COMMITTER_EMAIL: ci-user@github.local + GIT_COMMITTER_NAME: CI User + GIT_AUTHOR_EMAIL: ci-user@github.local + GIT_AUTHOR_NAME: CI User jobs: # Job to run linter / autoformat

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update CI badges for github actions

MODIFY README.md README.md # <a href="https://github.com/jupyterhub/repo2docker"><img src="https://raw.githubusercontent.com/jupyterhub/repo2docker/3fa7444fca6ae2b51e590cbc9d83baf92738ca2a/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> -[![Build Status](https://travis-ci.org/jupyterhub/repo2docker.svg?branch=master)](https://travis-ci.org/jupyterhub/repo2docker) +[![Deploy Status](https://travis-ci.org/jupyterhub/repo2docker.svg?branch=master)](https://travis-ci.org/jupyterhub/repo2docker) +[![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](![Continuous Integration](https://github.com/minrk/repo2docker/actions)) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) -[![Build Status](https://dev.azure.com/jupyterhub/repo2docker/_apis/build/status/jupyter.repo2docker?branchName=master)](https://dev.azure.com/jupyterhub/repo2docker/_build/latest?definitionId=1&branchName=master) [![Contribute](https://img.shields.io/badge/I_want_to_contribute!-grey?logo=jupyter)](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html) `repo2docker` fetches a git repository and builds a container image based on

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Handle requirements.txt with `--pre` lines This is a global flag which our inspection of requirements.txt files should ignore as it doesn't imply a local reference.

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -469,6 +469,10 @@ def is_local_pip_requirement(line): if line.startswith(("--requirement", "--constraint")): # as above but flags are spelt out return True + # the `--pre` flag is a global flag and should appear on a line by itself + # we just care that this isn't a "local pip requirement" + if line.startswith("--pre"): + return False # strip off things like `--editable=`. Long form arguments require a = if line.startswith("--"): line = line.split("=", 1)[1] MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -146,6 +146,8 @@ def test_open_guess_encoding(): ("git+https://github.com/jupyterhub/repo2docker", False), ("numpy", False), ("# -e .", False), + ("--pre", False), + ("--pre pandas", False), ], ) def test_local_pip_requirement(req, is_local):

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Add additional test cases and robuster parsing

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -473,14 +473,29 @@ def is_local_pip_requirement(line): # we just care that this isn't a "local pip requirement" if line.startswith("--pre"): return False + # strip off things like `--editable=`. Long form arguments require a = if line.startswith("--"): + # if splitting doesn't work it is probably because the line contains + # a syntax error or our "parser" is too simplistic so we return True + # just in case + try: line = line.split("=", 1)[1] + except IndexError: + return True + # strip off short form arguments like `-e`. Short form arguments can be # followed by a space `-e foo` or use `-e=foo`. The latter is not handled # here. We can deal with it when we see someone using it. if line.startswith("-"): + # if splitting doesn't work it is probably because the line contains + # a syntax error or our "parser" is too simplistic so we return True + # just in case + try: line = line.split(None, 1)[1] + except IndexError: + return True + if "file://" in line: # file references break isolation return True MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -147,7 +147,13 @@ def test_open_guess_encoding(): ("numpy", False), ("# -e .", False), ("--pre", False), + # pip ignores the package name and treats this like `--pre` on a line + # by itself ("--pre pandas", False), + # These are invalid lines as far as pip is concerned, check that our + # code is robust and continues running + ("--unrecognized", True), + ("-e", True), ], ) def test_local_pip_requirement(req, is_local):

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MODIFY README.md README.md # <a href="https://github.com/jupyterhub/repo2docker"><img src="https://raw.githubusercontent.com/jupyterhub/repo2docker/3fa7444fca6ae2b51e590cbc9d83baf92738ca2a/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> [![Deploy Status](https://travis-ci.org/jupyterhub/repo2docker.svg?branch=master)](https://travis-ci.org/jupyterhub/repo2docker) -[![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](![Continuous Integration](https://github.com/minrk/repo2docker/actions)) +[![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](https://github.com/jupyterhub/repo2docker/actions) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) [![Contribute](https://img.shields.io/badge/I_want_to_contribute!-grey?logo=jupyter)](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html)

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add www-frame-origin=same to /etc/rstudio/rserver.conf

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -309,7 +309,8 @@ class CondaBuildPack(BaseImage): r""" echo auth-none=1 >> /etc/rstudio/rserver.conf && \ echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \ - echo "rsession-which-r={0}/bin/R" >> /etc/rstudio/rserver.conf + echo "rsession-which-r={0}/bin/R" >> /etc/rstudio/rserver.conf && \ + echo www-frame-origin=same >> /etc/rstudio/rserver.conf """.format( env_prefix ),

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Unrecognised and invalid lines don't disable optimisation Lines in requirements files that we don't recognise or are syntax errors do not disable our "optimised" build process.

MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -152,8 +152,8 @@ def test_open_guess_encoding(): ("--pre pandas", False), # These are invalid lines as far as pip is concerned, check that our # code is robust and continues running - ("--unrecognized", True), - ("-e", True), + ("--unrecognized", False), + ("-e", False), ], ) def test_local_pip_requirement(req, is_local):

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Mercurial: use the full node id (12 characters) for the content_id

MODIFY repo2docker/contentproviders/mercurial.py repo2docker/contentproviders/mercurial.py @@ -66,14 +66,12 @@ class Mercurial(ContentProvider): ) raise ValueError("Failed to update to ref {}".format(ref)) - cmd = ["hg", "identify"] + cmd = ["hg", "identify", "-i"] cmd.extend(hg_config) sha1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, cwd=output_dir) - self._sha1 = sha1.stdout.read().decode().strip() + self._node_id = sha1.stdout.read().decode().strip() @property def content_id(self): - """A unique ID to represent the version of the content. - Uses the first seven characters of the git commit ID of the repository. - """ - return self._sha1[:7] + """A unique ID to represent the version of the content.""" + return self._node_id

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Add Mercurial+evolve in install_requires

MODIFY setup.py setup.py @@ -55,6 +55,8 @@ setup( "ruamel.yaml>=0.15", "toml", "semver", + "mercurial>=5.2; python_version > '3.5'", + "hg-evolve>=10.0; python_version > '3.5'", ], python_requires=">=3.6", author="Project Jupyter Contributors",

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Crosslink 'Configuring your repository' with usage

MODIFY docs/source/configuration/index.rst docs/source/configuration/index.rst @@ -5,6 +5,8 @@ Configuring your repository Information about configuring your repository to work with repo2docker, and controlling elements of the built environment using configuration files. +For information on where to put your configuration files see :ref:`usage-config-file-location`. + .. toctree:: :maxdepth: 2 :caption: Complete list of configuration files MODIFY docs/source/usage.rst docs/source/usage.rst @@ -79,6 +79,8 @@ specify the ``branch-name`` or ``commit-hash``. For example:: commit-hash will result in the latest commit of the repository being built. +.. _usage-config-file-location: + Where to put configuration files ================================

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Add workflow to build Docker image

ADD .github/workflows/docker.yml +name: Docker build + +on: + - push + - pull_request + +jobs: + docker: + runs-on: ubuntu-18.04 + steps: + - name: Checkout code + uses: actions/checkout@v2 + with: + fetch-depth: 0 + + # https://github.com/docker/build-push-action + - name: Build Docker image + uses: docker/build-push-action@v1 + with: + repository: jupyter/repo2docker + push: false + + - name: Run repo2docker Docker image + run: docker run jupyter/repo2docker repo2docker --version

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Docker workflow try adding tag

MODIFY .github/workflows/docker.yml .github/workflows/docker.yml @@ -18,7 +18,8 @@ jobs: uses: docker/build-push-action@v1 with: repository: jupyter/repo2docker + tags: pr push: false - name: Run repo2docker Docker image - run: docker run jupyter/repo2docker repo2docker --version + run: docker run jupyter/repo2docker:pr repo2docker --version

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Fix bug hg id topic

MODIFY tests/unit/contentproviders/test_mercurial.py tests/unit/contentproviders/test_mercurial.py @@ -146,7 +146,7 @@ def test_ref_topic(hg_repo_with_content): """ upstream, node_id = hg_repo_with_content node_id = subprocess.Popen( - ["hg", "identify", "-i", "-r", "topic(test-topic)"], + ["hg", "identify", "-i", "-r", "topic(test-topic)"] + args_enabling_topic, stdout=subprocess.PIPE, cwd=upstream, )

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Disable jupyterlab extension build minimize

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -48,8 +48,13 @@ conda env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml # This will install and enable the extension for jupyter notebook ${NB_PYTHON_PREFIX}/bin/python -m pip install jupyter-offlinenotebook==0.1.0 # and this installs it for lab. Keep going if the lab version is incompatible -# with the extension -${NB_PYTHON_PREFIX}/bin/jupyter labextension install jupyter-offlinenotebook || true +# with the extension. +# Don't minimize build as it may fail, possibly due to excessive resource usage +# https://discourse.jupyter.org/t/tip-binder-jupyterlab-extension/6022 +# https://discourse.jupyter.org/t/jupyter-lab-build-hangs-and-then-fails-at-webpack-config-webpack-prod-minimize-config-js/6017/3 +${NB_PYTHON_PREFIX}/bin/jupyter labextension install --no-build jupyter-offlinenotebook && \ +$NB_PYTHON_PREFIX/bin/jupyter lab build --minimize=False || \ +true # empty conda history file, # which seems to result in some effective pinning of packages in the initial env,

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Fix shell syntax error with time

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -294,8 +294,8 @@ class CondaBuildPack(BaseImage): ( "${NB_USER}", r""" - time mamba install -p {0} r-base{1} r-irkernel={2} r-devtools && \ - time mamba clean --all -f -y && \ + mamba install -p {0} r-base{1} r-irkernel={2} r-devtools && \ + mamba clean --all -f -y && \ mamba list -p {0} """.format( env_prefix, r_pin, IRKERNEL_VERSION

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One more time (pun intended)

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -61,7 +61,7 @@ time ${NB_PYTHON_PREFIX}/bin/python -m pip install jupyter-offlinenotebook==0.1. # https://discourse.jupyter.org/t/tip-binder-jupyterlab-extension/6022 # https://discourse.jupyter.org/t/jupyter-lab-build-hangs-and-then-fails-at-webpack-config-webpack-prod-minimize-config-js/6017/3 time ${NB_PYTHON_PREFIX}/bin/jupyter labextension install --no-build jupyter-offlinenotebook && \ -$NB_PYTHON_PREFIX/bin/jupyter lab build --minimize=False || \ +time $NB_PYTHON_PREFIX/bin/jupyter lab build --minimize=False || \ true # empty conda history file,

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conda: set TIMEFORMAT for timed bash commands

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -79,6 +79,7 @@ class CondaBuildPack(BaseImage): ( "root", r""" + TIMEFORMAT='time: %3R' \ bash -c 'time /tmp/install-miniforge.bash' && \ rm /tmp/install-miniforge.bash /tmp/environment.yml """, @@ -275,6 +276,7 @@ class CondaBuildPack(BaseImage): ( "${NB_USER}", r""" + TIMEFORMAT='time: %3R' \ bash -c 'time mamba env update -p {0} -f "{1}" && \ time mamba clean --all -f -y && \ mamba list -p {0} \

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update docs for config dirs

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -90,8 +90,8 @@ Where to put configuration files * A folder named ``.binder/`` in the root of the repository. * The root directory of the repository. -`repo2docker` searches for these folders in order (``binder/``, ``.binder/``, -root). Only configuration files in the first identified folder are considered. +Having both ``binder/`` and ``.binder/`` folders is not allowed. +And if one of these folders exists, configuration files in that folder are considered only. Check the complete list of :ref:`configuration files <config-files>` supported by ``repo2docker`` to see how to configure the build process.

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Update docs/source/usage.rst

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -91,7 +91,7 @@ Where to put configuration files * The root directory of the repository. Having both ``binder/`` and ``.binder/`` folders is not allowed. -And if one of these folders exists, configuration files in that folder are considered only. +If one of these folders exists, only configuration files in that folder are considered, configuration in the root directory will be ignored. Check the complete list of :ref:`configuration files <config-files>` supported by ``repo2docker`` to see how to configure the build process.

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add chown to COPY commands to reduce layer count

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -100,7 +100,7 @@ ENV PATH {{ ':'.join(path) }}:${PATH} {% if build_script_files -%} # If scripts required during build are present, copy them {% for src, dst in build_script_files|dictsort %} -COPY {{ src }} {{ dst }} +COPY --chown=${NB_USER}:${NB_USER} {{ src }} {{ dst }} {% endfor -%} {% endif -%} @@ -137,24 +137,16 @@ ENV {{item[0]}} {{item[1]}} {% if preassemble_script_files -%} # If scripts required during build are present, copy them {% for src, dst in preassemble_script_files|dictsort %} -COPY src/{{ src }} ${REPO_DIR}/{{ dst }} +COPY --chown=${NB_USER}:${NB_USER} src/{{ src }} ${REPO_DIR}/{{ dst }} {% endfor -%} {% endif -%} -{% if preassemble_script_directives -%} -USER root -RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} -{% endif -%} - {% for sd in preassemble_script_directives -%} {{ sd }} {% endfor %} -# Copy and chown stuff. This doubles the size of the repo, because -# you can't actually copy as USER, only as root! Thanks, Docker! -USER root -COPY src/ ${REPO_DIR} -RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} +# Copy stuff. +COPY --chown=${NB_USER}:${NB_USER} src/ ${REPO_DIR} # Run assemble scripts! These will actually turn the specification # in the repository into an image.

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Ensure REPO_DIR owned by NB_USER

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -113,6 +113,7 @@ COPY --chown={{ user }}:{{ user }} {{ src }} {{ dst }} ARG REPO_DIR=${HOME} ENV REPO_DIR ${REPO_DIR} WORKDIR ${REPO_DIR} +RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR} # We want to allow two things: # 1. If there's a .local/bin directory in the repo, things there

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Add test for writable permission on REPO_DIR

MODIFY tests/conda/repo-path/verify tests/conda/repo-path/verify @@ -13,5 +13,8 @@ assert sys.executable.startswith("/srv/conda/"), sys.executable assert os.path.exists("/srv/repo/verify") assert os.path.abspath(__file__) == "/srv/repo/verify" +# 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

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Remove reference to `master` branch from CLI doc

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -96,7 +96,8 @@ def get_argparser(): argparser.add_argument( "--ref", help=( - "If building a git url, which reference to check out. " "E.g., `master`." + "Reference to build instead of default reference. For example" + " branch name or commit for a Git repository." ), )

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Add explicit error message when `master` is specified Provide a specific error messaeg with a hint towards solution when a user specifies `master` as ref and we can't find it.

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -47,9 +47,18 @@ class Git(ContentProvider): self.log.error( "Failed to check out ref %s", ref, extra=dict(phase="failed") ) - raise ValueError("Failed to check out ref {}".format(ref)) + if ref == "master": + msg = ( + "Failed to check out the 'master' branch. " + "Maybe the default branch is not named 'master' " + "for this repository.\n\nTry not explicitly " + "specifying `--ref`." + ) + else: + msg = "Failed to check out ref {}".format(ref) + raise ValueError(msg) # We don't need to explicitly checkout things as the reset will - # take of that. If the hash is resolved above, we should be + # take care of that. If the hash is resolved above, we should be # able to reset to it for line in execute_cmd( ["git", "reset", "--hard", hash], cwd=output_dir, capture=yield_output

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regression test for specifying channel name in enviornment.yml dependency this didn't work with mamba 0.5

ADD tests/conda/channel-dep/environment.yml +name: lume-model-server-demo +dependencies: + - python=3.7 + # specify a channel name in the dependency + # mamba < 0.6 doesn't handle this right + - bokeh::jupyter_bokeh==2.0.3 ADD tests/conda/channel-dep/verify +#!/usr/bin/env python3 +import jupyter_bokeh

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Update to node 14

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -57,8 +57,8 @@ RUN groupadd \ RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ DISTRO="bionic" && \ - echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \ - echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list + echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \ + echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list # Base package installs are not super interesting to users, so hide their outputs # If install fails for some reason, errors will still be printed ADD tests/base/node/README.md +Test that node 12 and npm 6 are installed and runnable. RENAME tests/base/node10/verify tests/base/node/verify @@ -5,7 +5,7 @@ set -ex # check node system package and its version which node node --version -node --version | grep v10 +node --version | grep v14 which npm npm --version DELETE tests/base/node10/README.md -Test that node 10 and npm 6 are installed and runnable.

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Stream jupyter server logs to a file By streaming the logs also to a file users can access them from inside the container which helps them debug issues without having to ask an admin.

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint # lightest possible entrypoint that ensures that # we use a login shell to get a fully configured shell environment # (e.g. sourcing /etc/profile.d, ~/.bashrc, and friends) + +# Setup a file descriptor (FD) that is connected to a tee process which +# writes its input to $REPO_DIR/.jupyter-server-log.txt +# We later use this FD as a place to redirect the output of the actual +# command to. We can't add `tee` to the command directly as that will prevent +# the container from exiting when `docker stop` is run. +exec {log_fd}> >(exec tee $REPO_DIR/.jupyter-server-log.txt) + if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then if [[ ! -x "$R2D_ENTRYPOINT" ]]; then chmod u+x "$R2D_ENTRYPOINT" fi - exec "$R2D_ENTRYPOINT" "$@" + exec "$R2D_ENTRYPOINT" "$@" >&"$log_fd" 2>&1 else - exec "$@" + exec "$@" >&"$log_fd" 2>&1 fi

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Add StackOverflow link to comment

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint # We later use this FD as a place to redirect the output of the actual # command to. We can't add `tee` to the command directly as that will prevent # the container from exiting when `docker stop` is run. +# See https://stackoverflow.com/a/55678435 exec {log_fd}> >(exec tee $REPO_DIR/.jupyter-server-log.txt) if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then

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Ensure output arrives on stderr

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint @@ -15,10 +15,10 @@ if [[ ! -z "${R2D_ENTRYPOINT:-}" ]]; then if [[ ! -x "$R2D_ENTRYPOINT" ]]; then chmod u+x "$R2D_ENTRYPOINT" fi - exec "$R2D_ENTRYPOINT" "$@" >&"$log_fd" 2>&1 + exec "$R2D_ENTRYPOINT" "$@" >&"$log_fd" else - exec "$@" >&"$log_fd" 2>&1 + exec "$@" >&"$log_fd" fi -# Close the loggging output aggain -exec {log_fd}>&- +# Close the logging output again +#exec {log_fd}>&- MODIFY tests/unit/test_env.py tests/unit/test_env.py @@ -58,6 +58,10 @@ def test_env(): # all docker output is returned by repo2docker on stderr # extract just the declare for better failure message formatting + # stdout should be empty + assert not result.stdout + + # stderr should contain lines of output declares = [x for x in result.stderr.split("\n") if x.startswith("declare")] assert 'declare -x FOO="{}"'.format(ts) in declares assert 'declare -x BAR="baz"' in declares

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Update mamba to latest

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -6,6 +6,7 @@ set -ex cd $(dirname $0) MINIFORGE_VERSION=4.9.2-2 +MAMBA_VERSION=0.7.4 # SHA256 for installers can be obtained from https://github.com/conda-forge/miniforge/releases SHA256SUM="7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc" @@ -41,6 +42,8 @@ echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc # avoid future changes to default channel_priority behavior conda config --system --set channel_priority "flexible" +time mamba install -y mamba==${MAMBA_VERSION} + echo "installing notebook env:" cat /tmp/environment.yml time mamba env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml

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buildpacks/nix: 2.3 -> 2.3.9 Update to latest version.

MODIFY repo2docker/buildpacks/nix/install-nix.bash repo2docker/buildpacks/nix/install-nix.bash # This downloads and installs a pinned version of nix set -ex -NIX_VERSION="2.3" -NIX_SHA256="e43f6947d1f302b6193302889e7800f3e3dd4a650b6f929c668c894884a02701" +NIX_VERSION="2.3.9" +NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4" # Do all our operations in /tmp, since we can't rely on current directory being writeable yet. cd /tmp

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Allow extra path in figshare URLs Copied from

MODIFY repo2docker/contentproviders/figshare.py repo2docker/contentproviders/figshare.py @@ -39,7 +39,7 @@ class Figshare(DoiProvider): } ] - url_regex = re.compile(r"(.*)/articles/([^/]+)/(\d+)(/)?(\d+)?") + url_regex = re.compile(r"(.*)/articles/([^/]+)/([^/]+)/(\d+)(/)?(\d+)?") def detect(self, doi, ref=None, extra_args=None): """Trigger this provider for things that resolve to a Figshare article""" @@ -53,8 +53,8 @@ class Figshare(DoiProvider): if any([url.startswith(s) for s in host["hostname"]]): match = self.url_regex.match(url) if match: - self.article_id = match.groups()[2] - self.article_version = match.groups()[4] + self.article_id = match.groups()[3] + self.article_version = match.groups()[5] if not self.article_version: self.article_version = "1" return {

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Can't just use '([^/]+)/' for the new figshare url This may break detection of non-code URLs

MODIFY repo2docker/contentproviders/figshare.py repo2docker/contentproviders/figshare.py @@ -39,7 +39,7 @@ class Figshare(DoiProvider): } ] - url_regex = re.compile(r"(.*)/articles/([^/]+)/([^/]+)/(\d+)(/)?(\d+)?") + url_regex = re.compile(r"(.*)/articles/(code/)?([^/]+)/(\d+)(/)?(\d+)?") def detect(self, doi, ref=None, extra_args=None): """Trigger this provider for things that resolve to a Figshare article"""

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Bug in figshare? It looks like the new figshare redirects may drop the version suffix causing two tests to fail (see the test comments).

MODIFY tests/unit/contentproviders/test_figshare.py tests/unit/contentproviders/test_figshare.py @@ -50,10 +50,16 @@ test_dois_links = [ ( "https://doi.org/10.6084/m9.figshare.9782777.v1", {"host": test_fig.hosts[0], "article": "9782777", "version": "1"}, + # $ curl -sIL https://doi.org/10.6084/m9.figshare.9782777.v1 | grep location + # location: https://figshare.com/articles/Binder-ready_openSenseMap_Analysis/9782777/1 + # location: https://figshare.com/articles/code/Binder-ready_openSenseMap_Analysis/9782777 ), ( "https://doi.org/10.6084/m9.figshare.9782777.v3", {"host": test_fig.hosts[0], "article": "9782777", "version": "3"}, + # $ curl -sIL https://doi.org/10.6084/m9.figshare.9782777.v3 | grep location + # location: https://figshare.com/articles/Binder-ready_openSenseMap_Analysis/9782777/3 + # location: https://figshare.com/articles/code/Binder-ready_openSenseMap_Analysis/9782777 ), ( "https://figshare.com/articles/title/97827771234",

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figshare article types: code and dataset

MODIFY repo2docker/contentproviders/figshare.py repo2docker/contentproviders/figshare.py @@ -39,7 +39,10 @@ class Figshare(DoiProvider): } ] - url_regex = re.compile(r"(.*)/articles/(code/)?([^/]+)/(\d+)(/)?(\d+)?") + # We may need to add other item types in future, see + # https://github.com/jupyterhub/repo2docker/pull/1001#issuecomment-760107436 + # for a list + url_regex = re.compile(r"(.*)/articles/(code/|dataset/)?([^/]+)/(\d+)(/)?(\d+)?") def detect(self, doi, ref=None, extra_args=None): """Trigger this provider for things that resolve to a Figshare article"""

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Fix the docker image name generation make sure all the parts that constitute the generated docker image name are escaped, otherwise the docker building process can fail (with a rather hard to understand error). Before this fix, the `provider.content_id` was not escaped.

MODIFY repo2docker/app.py repo2docker/app.py @@ -401,20 +401,19 @@ class Repo2Docker(Application): self.log.info(log_line, extra=dict(phase="fetching")) if not self.output_image_spec: - self.output_image_spec = ( - "r2d" + escapism.escape(self.repo, escape_char="-").lower() - ) + image_spec = "r2d" + self.repo # if we are building from a subdirectory include that in the # image name so we can tell builds from different sub-directories # apart. if self.subdir: - self.output_image_spec += escapism.escape( - self.subdir, escape_char="-" - ).lower() + image_spec += self.subdir if picked_content_provider.content_id is not None: - self.output_image_spec += picked_content_provider.content_id + image_spec += picked_content_provider.content_id else: - self.output_image_spec += str(int(time.time())) + image_spec += str(int(time.time())) + self.output_image_spec = escapism.escape( + image_spec, escape_char="-" + ).lower() def json_excepthook(self, etype, evalue, traceback): """Called on an uncaught exception when using json logging

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Mention the SWHID source-repository format in the usage documentation

MODIFY docs/source/usage.rst docs/source/usage.rst @@ -14,6 +14,8 @@ Using ``repo2docker`` follows :ref:`specification`. repo2docker is called with the URL of a Git repository, a `DOI <https://en.wikipedia.org/wiki/Digital_object_identifier>`_ from Zenodo or Figshare, a `Handle <https://en.wikipedia.org/wiki/Handle_System>`_ or DOI from a Dataverse installation, +a `SWHID`_ of a directory of a revision archived in the +`Software Heritage Archive <https://archive.softwareheritage.org>`_, or a path to a local directory. It then performs these steps: @@ -36,7 +38,8 @@ repo2docker is called with this command:: where ``<source-repository>`` is: * a URL of a Git repository (``https://github.com/binder-examples/requirements``), - * a Zenodo DOI (``10.5281/zenodo.1211089``), or + * a Zenodo DOI (``10.5281/zenodo.1211089``), + * a SWHID_ (``swh:1:rev:999dd06c7f679a2714dfe5199bdca09522a29649``), or * a path to a local directory (``a/local/directory``) of the source repository you want to build. @@ -132,3 +135,4 @@ Command line API .. _Pytudes: https://github.com/norvig/pytudes +.. _SWHID: https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html

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Update comment about travis steps We no longer run tests on the code so we would not spot missing files or problems with the wheel we build.

MODIFY .travis.yml .travis.yml @@ -7,8 +7,7 @@ services: python: - 3.8 install: -# Make a wheel and install it to test to catch possible -# issues with releases +# Make a wheel and install it - pip install --upgrade setuptools pip - pip install -r dev-requirements.txt - python setup.py bdist_wheel

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Remove changelog reference

MODIFY CONTRIBUTING.md CONTRIBUTING.md @@ -23,4 +23,4 @@ There are a few other pages to highlight: Its a good place to understand _why_ the team have made the decisions that they have along the way! * We absolutely encourage discussion around refactoring, updating or extending repo2docker, but please make sure that you've understood this page before opening an issue to discuss the change you'd like to propose. * [Common developer tasks and how-tos](https://repo2docker.readthedocs.io/en/latest/contributing/tasks.html) - * Some notes on running tests, buildpack dependencies, creating a release, updating the changelog and keeping the pip files up to date. + * Some notes on running tests, buildpack dependencies, creating a release, and keeping the pip files up to date.

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Remove travis CI configuration All tests have been migrated to other CI providers so we can turn travis off completely.

DELETE .travis.yml -dist: xenial -os: linux -language: python -cache: pip -services: -- docker -python: -- 3.8 -install: -# Make a wheel and install it -- pip install --upgrade setuptools pip -- pip install -r dev-requirements.txt -- python setup.py bdist_wheel -- pip install dist/*.whl -- pip freeze -script: -- | - # run autoformat - if [[ "$REPO_TYPE" == "lint" ]]; then - pre-commit run --all-files - fi -after_success: -- pip install codecov -- pushd tests && codecov && popd - -after_failure: -- | - # point to auto-lint-fix - echo "You can install pre-commit hooks to automatically run formatting" - echo "on each commit with:" - echo " pre-commit install" - echo "or you can run by hand on staged files with" - echo " pre-commit run" - echo "or after-the-fact on already committed files with" - echo " pre-commit run --all-files"

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Experiment with different install mechanism to get coverage

MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -106,7 +106,8 @@ jobs: pip install --upgrade setuptools pip wheel pip install --upgrade -r dev-requirements.txt python setup.py bdist_wheel - pip install dist/*.whl + #pip install dist/*.whl + pip install -e. pip freeze # hg-evolve pinned to 9.2 because hg-evolve dropped support for # hg 4.5, installed with apt in Ubuntu 18.04

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Specify coverage rule to combine results We can specify a rule to map different source files from which coverage stats were collected to the same source file in our repository.

MODIFY .coveragerc .coveragerc [run] # this file comes from versioneer and we don't test it omit = */_version.py + +[paths] +# This tells coverage how to combine results together or said differently +# which files at different paths are actually the same file +# documented at https://coverage.readthedocs.io/en/latest/config.html#paths +source = + repo2docker/ + /opt/hostedtoolcache/Python/*/site-packages/repo2docker MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -106,8 +106,7 @@ jobs: pip install --upgrade setuptools pip wheel pip install --upgrade -r dev-requirements.txt python setup.py bdist_wheel - #pip install dist/*.whl - pip install -e. + pip install dist/*.whl pip freeze # hg-evolve pinned to 9.2 because hg-evolve dropped support for # hg 4.5, installed with apt in Ubuntu 18.04

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Changeg source file aliasing

MODIFY .coveragerc .coveragerc @@ -6,6 +6,11 @@ omit = */_version.py # This tells coverage how to combine results together or said differently # which files at different paths are actually the same file # documented at https://coverage.readthedocs.io/en/latest/config.html#paths +# Yes, we list repo2docker twice here. This allows you to install repo2docker +# with `pip install -e.` for local development and from the wheel (as done on +# CI) and get `repo2docker/foo.py` as paths in the coverage report source = - repo2docker/ - /opt/hostedtoolcache/Python/*/site-packages/repo2docker + repo2docker + repo2docker + ../repo2docker + */site-packages/repo2docker MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -114,7 +114,10 @@ jobs: - name: "Run tests" run: | - pytest --durations 10 --cov repo2docker -v tests/${{ matrix.repo_type }} + cd tests + pytest --durations 10 --cov repo2docker -v ${{ matrix.repo_type }} # Action Repo: https://github.com/codecov/codecov-action - uses: codecov/codecov-action@v1 + with: + directory: ./tests

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Use Python codecov package instead of GH action We can't set the working directory of the GH Action which means we need to install codecov ourselves and run it in the `tests/` sub-directory.

MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -117,8 +117,7 @@ jobs: cd tests pytest --durations 10 --cov repo2docker -v ${{ matrix.repo_type }} - # Action Repo: https://github.com/codecov/codecov-action - - uses: codecov/codecov-action@v1 - working-directory: ./tests - with: - directory: ./tests + - name: "Upload code coverage stats" + run: | + pip install codecov + pushd tests && codecov && popd

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Fix/rewrite paths for codecov filename matching

MODIFY .codecov.yml .codecov.yml # show coverage in CI status, not as a comment. comment: off +fixes: + - "*/site-packages/::" coverage: status: project: MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -120,4 +120,5 @@ jobs: - name: "Upload code coverage stats" run: | pip install codecov - pushd tests && codecov && popd + pushd tests && codecov && cat + cat /home/runner/work/repo2docker/repo2docker/tests/coverage.xml

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bump python in docs tests

MODIFY .circleci/config.yml .circleci/config.yml @@ -4,7 +4,7 @@ jobs: build_docs: # This is the base environment that Circle will use docker: - - image: circleci/python:3.6-stretch + - image: circleci/python:3.8-buster steps: # Get our data and merge with upstream - run: sudo apt-get update

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entrypoint needs to run on py35

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint #!/usr/bin/env python3 +# note: must run on Python >= 3.5 # goals: # - load environment variables from a login shell (bash -l) @@ -35,7 +36,7 @@ def get_login_env(): try: return json.loads(last_line) except Exception as e: - print(f"Error getting login env: {e}", file=sys.stderr) + print("Error getting login env: {e}".format(e=e), file=sys.stderr) return {} @@ -113,7 +114,11 @@ def main(): def relay_signal(sig, frame): """Relay a signal to children""" - print(f"Forwarding signal {sig} to {child_pgid}") + print( + "Forwarding signal {sig} to {child_pgid}".format( + sig=sig, child_pgid=child_pgid + ) + ) os.killpg(child_pgid, sig) # question: maybe use all valid_signals() except a few, e.g. SIGCHLD?

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bump notebook, nbconvert, jupyterhub jupyterhub-singleuser==1.3.0 nbconvert==6.0.7 notebook==6.2.0

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -4,7 +4,7 @@ dependencies: - jupyter-offlinenotebook==0.2.1 - jupyter-resource-usage==0.5.1 - jupyterlab==3.0.7 - - jupyterhub-singleuser==1.1.0 - - nbconvert==5.6.1 - - notebook==6.1.6 + - jupyterhub-singleuser==1.3.0 + - nbconvert==6.0.7 + - notebook==6.2.0 - nteract_on_jupyter==2.1.3

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handle $R2D_ENTRYPOINT in new entrypoint

MODIFY repo2docker/buildpacks/repo2docker-entrypoint repo2docker/buildpacks/repo2docker-entrypoint #!/usr/bin/env python3 -# note: must run on Python >= 3.5 +# note: must run on Python >= 3.5, which mainly means no f-strings # goals: # - load environment variables from a login shell (bash -l) @@ -84,8 +84,13 @@ def main(): "a", ) + command = sys.argv[1:] + r2d_entrypoint = os.environ.get("R2D_ENTRYPOINT") + if r2d_entrypoint: + command.insert(0, r2d_entrypoint) + child = subprocess.Popen( - sys.argv[1:], + command, bufsize=1, env=env, start_new_session=True,

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bump docker action to v2 tags/repository are merged set context

MODIFY .github/workflows/docker.yml .github/workflows/docker.yml @@ -15,10 +15,10 @@ jobs: # https://github.com/docker/build-push-action - name: Build Docker image - uses: docker/build-push-action@v1 + uses: docker/build-push-action@v2 with: - repository: jupyter/repo2docker - tags: pr + context: . + tags: jupyter/repo2docker:pr push: false - name: Run repo2docker Docker image

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buildpacks.r: dont use apt-key directly to respect *_proxy env vars

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -247,12 +247,12 @@ class RBuildPack(PythonBuildPack): echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran{vs}/" > /etc/apt/sources.list.d/r-ubuntu.list """, ), - # Use port 80 to talk to the keyserver to increase the chances + # Dont use apt-key directly, as gpg does not always respect *_proxy vars. This increase the chances # of being able to reach it from behind a firewall ( "root", r""" - apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 + wget --quiet -O - 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9' | apt-key add - """, ), (

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Catch errors on fetching Julia versions

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -18,9 +18,12 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): @property @functools.lru_cache(maxsize=1) def all_julias(self): + try: json = requests.get( "https://julialang-s3.julialang.org/bin/versions.json" ).json() + except Exception as e: + raise RuntimeError("Failed to fetch available Julia versions: {e}") vers = [semver.VersionInfo.parse(v) for v in json.keys()] # filter out pre-release versions not supported by find_semver_match() filtered_vers = [v for v in vers if v.prerelease is None]

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Manually specify default compat version 1.5

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -41,18 +41,18 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): else: project_toml = toml.load(self.binder_path("Project.toml")) - if "compat" in project_toml: - if "julia" in project_toml["compat"]: - julia_version_str = project_toml["compat"]["julia"] - + try: # For Project.toml files, install the latest julia version that # satisfies the given semver. - _julia_version = find_semver_match(julia_version_str, self.all_julias) - if _julia_version is not None: - return _julia_version - - default_julia_version = self.all_julias[-1] - return default_julia_version + compat = project_toml["compat"]["julia"] + except: + # Default version which needs to be manually updated with new major.minor releases + compat = "1.5" + + match = find_semver_match(compat, self.all_julias) + if match is None: + raise RuntimeError("Failed to find a matching Julia version: {compat}") + return match def get_build_env(self): """Get additional environment settings for Julia and Jupyter

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setup.py: install_requires in alphabetical order

MODIFY setup.py setup.py @@ -48,14 +48,14 @@ setup( version=versioneer.get_version(), install_requires=[ "docker", - "traitlets", - "python-json-logger", "escapism", "jinja2", + "python-json-logger", "requests", "ruamel.yaml>=0.15", - "toml", "semver", + "toml", + "traitlets", ], python_requires=">=3.6", author="Project Jupyter Contributors",

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freeze with strict channel priority avoids pulling in newer releases from defaults this is conda's default behavior, but not mamba's

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -77,6 +77,7 @@ def freeze(env_file, frozen_file): "; ".join( [ "set -ex", + "conda config --set channel_priority strict", "conda config --add channels conda-forge", f"mamba install -yq -S mamba={MAMBA_VERSION}" if MAMBA_VERSION

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explicitly put pip in the base env instead of depending on conda's automatic pip dependency for Python, which is sensitive to configuation

MODIFY repo2docker/buildpacks/conda/environment.py-2.7.yml repo2docker/buildpacks/conda/environment.py-2.7.yml @@ -2,5 +2,6 @@ channels: - conda-forge dependencies: - python=2.7.* +- pip - ipykernel==4.8.2 - wcwidth==0.1.9 MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -2,6 +2,7 @@ channels: - conda-forge dependencies: - python=3.7 + - pip - ipywidgets==7.6.3 - jupyter-offlinenotebook==0.2.1 - jupyter-resource-usage==0.5.1

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use mamba create instead of mamba env create I'm never sure what the difference is, but mamba env create doesn't accept explicit dependency format

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -46,7 +46,7 @@ time mamba install -y mamba==${MAMBA_VERSION} echo "installing notebook env:" cat /tmp/environment.yml -time mamba env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml +time mamba create --prefix ${NB_PYTHON_PREFIX} --file /tmp/environment.yml # empty conda history file, # which seems to result in some effective pinning of packages in the initial env, @@ -59,7 +59,7 @@ if [[ -f /tmp/kernel-environment.yml ]]; then echo "installing kernel env:" cat /tmp/kernel-environment.yml - time mamba env create -p ${KERNEL_PYTHON_PREFIX} -f /tmp/kernel-environment.yml + time mamba create --prefix ${KERNEL_PYTHON_PREFIX} --file /tmp/kernel-environment.yml ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}" echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history mamba list -p ${KERNEL_PYTHON_PREFIX}

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Fix logo URL in README

MODIFY README.md README.md -# <a href="https://github.com/jupyterhub/repo2docker"><img src="https://raw.githubusercontent.com/jupyterhub/repo2docker/3fa7444fca6ae2b51e590cbc9d83baf92738ca2a/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> +# <a href="https://github.com/jupyterhub/repo2docker"><img src="https://raw.githubusercontent.com/jupyterhub/repo2docker/8731ecf0967cc5fde028c456f2b92be651ebbc18/docs/source/_static/images/repo2docker.png" height="48px" /> repo2docker</a> [![Deploy Status](https://travis-ci.org/jupyterhub/repo2docker.svg?branch=master)](https://travis-ci.org/jupyterhub/repo2docker) [![Build Status](https://github.com/jupyterhub/repo2docker/workflows/Continuous%20Integration/badge.svg)](https://github.com/jupyterhub/repo2docker/actions)

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Set default Julia version to 1.6

MODIFY repo2docker/buildpacks/julia/julia_project.py repo2docker/buildpacks/julia/julia_project.py @@ -47,7 +47,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): compat = project_toml["compat"]["julia"] except: # Default version which needs to be manually updated with new major.minor releases - compat = "1.5" + compat = "1.6" match = find_semver_match(compat, self.all_julias) if match is None:

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install latest hg and hg evolve in CI

MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -110,7 +110,8 @@ jobs: pip freeze # hg-evolve pinned to 9.2 because hg-evolve dropped support for # hg 4.5, installed with apt in Ubuntu 18.04 - $(hg debuginstall --template "{pythonexe}") -m pip install hg-evolve==9.2 --user + pip install mercurial + $(hg debuginstall --template "{pythonexe}") -m pip install hg-evolve --user - name: "Run tests" run: |

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install setup-tools for hg

MODIFY .github/workflows/test.yml .github/workflows/test.yml @@ -110,8 +110,8 @@ jobs: pip freeze # hg-evolve pinned to 9.2 because hg-evolve dropped support for # hg 4.5, installed with apt in Ubuntu 18.04 - pip install mercurial - $(hg debuginstall --template "{pythonexe}") -m pip install hg-evolve --user + $(hg debuginstall --template "{pythonexe}") -m pip install setuptools --user + $(hg debuginstall --template "{pythonexe}") -m pip install hg-evolve==9.2 --user - name: "Run tests" run: |

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State newly used installation command `install_local` is used since

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -142,7 +142,7 @@ We use ``apt.txt``, for example, to install LaTeX in our 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_git(".")``. +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

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Add study participation notice to readme

MODIFY README.md README.md @@ -16,6 +16,19 @@ For support questions please search or post to https://discourse.jupyter.org/c/b See the [contributing guide](CONTRIBUTING.md) for information on contributing to repo2docker. +--- + +Please note that this repository is participating in a study into sustainability +of open source projects. Data will be gathered about this repository for +approximately the next 12 months, starting from 2021-06-11. + +Data collected will include number of contributors, number of PRs, time taken to +close/merge these PRs, and issues closed. + +For more information, please visit +[our informational page](https://sustainable-open-science-and-software.github.io/) or download our [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf). + +--- ## Using repo2docker ### Prerequisites

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Add build-base to build stage of docker image ruamel.yaml depends on ruamel.yaml.clib, which requires compilation on alpine. It did not seem to require the packages in build-base before, but it does now.

MODIFY Dockerfile Dockerfile ARG ALPINE_VERSION=3.12.0 FROM alpine:${ALPINE_VERSION} -RUN apk add --no-cache git python3 python3-dev py-pip +RUN apk add --no-cache git python3 python3-dev py-pip build-base # build wheels in first image ADD . /tmp/src

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Stop using deprecated add_stylesheet in sphinx add_stylesheet has been deprecated for a while. This should hopefully fix the CI failures in circleci

MODIFY docs/source/conf.py docs/source/conf.py @@ -47,7 +47,7 @@ from recommonmark.transform import AutoStructify def setup(app): - app.add_stylesheet("custom.css") # may also be a URL + app.add_css_file("custom.css") # may also be a URL app.add_config_value( "recommonmark_config", {"auto_toc_tree_section": "Contents"}, True )

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Handle attrs["State"]["ExitCode"]

MODIFY repo2docker/app.py repo2docker/app.py @@ -607,7 +607,7 @@ class Repo2Docker(Application): if container.status == "running": self.log.info("Stopping container...\n", extra=dict(phase="running")) container.kill() - exit_code = container.attrs["State"]["ExitCode"] + exit_code = container.exitcode container.wait() MODIFY repo2docker/docker.py repo2docker/docker.py @@ -25,6 +25,10 @@ class DockerContainer(Container): def stop(self, *, timeout=10): return self._c.stop(timeout=timeout) + @property + def exitcode(self): + return self._c.attrs["State"]["ExitCode"] + @property def status(self): return self._c.status MODIFY repo2docker/engine.py repo2docker/engine.py @@ -62,6 +62,13 @@ class Container(ABC): timeout : If the container doesn't gracefully stop after this timeout kill it """ + @property + @abstractmethod + def exitcode(self): + """ + The container exit code if exited + """ + @property @abstractmethod def status(self): MODIFY tests/unit/test_ports.py tests/unit/test_ports.py @@ -77,7 +77,7 @@ def read_port_mapping_response( container.reload() assert container.status == "running" - port_mapping = container.attrs["NetworkSettings"]["Ports"] + port_mapping = container._c.attrs["NetworkSettings"]["Ports"] if all_ports: port = port_mapping["8888/tcp"][0]["HostPort"]

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Python 3.5: can't have trailing , in function arg list

MODIFY repo2docker/docker.py repo2docker/docker.py @@ -61,7 +61,7 @@ class DockerEngine(ContainerEngine): # decode=False, dockerfile="", fileobj=None, - path="", + path="" ): return self._apiclient.build( buildargs=buildargs, @@ -96,7 +96,7 @@ class DockerEngine(ContainerEngine): ports=None, publish_all_ports=False, remove=False, - volumes=None, + volumes=None ): container = self._client.containers.run( image_spec, MODIFY repo2docker/engine.py repo2docker/engine.py @@ -107,7 +107,7 @@ class ContainerEngine(ABC): # decode=False, dockerfile="", fileobj=None, - path="", + path="" ): """ Build a container @@ -199,7 +199,7 @@ class ContainerEngine(ABC): ports={}, publish_all_ports=False, remove=False, - volumes={}, + volumes={} ): """ Run a container

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BuildError only takes positional params

MODIFY repo2docker/app.py repo2docker/app.py @@ -774,7 +774,7 @@ class Repo2Docker(Application): self.log.info(l["stream"], extra=dict(phase="building")) elif "error" in l: self.log.info(l["error"], extra=dict(phase="failure")) - raise BuildError(l["error"], build_log="") + raise BuildError(l["error"]) elif "status" in l: self.log.info( "Fetching base image...\r", extra=dict(phase="building")

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Container .build .run need to support **kwargs

MODIFY repo2docker/docker.py repo2docker/docker.py @@ -61,7 +61,8 @@ class DockerEngine(ContainerEngine): custom_context=False, dockerfile="", fileobj=None, - path="" + path="", + **kwargs, ): return self._apiclient.build( buildargs=buildargs, @@ -75,6 +76,7 @@ class DockerEngine(ContainerEngine): dockerfile=dockerfile, fileobj=fileobj, path=path, + **kwargs, ) def images(self): @@ -96,7 +98,8 @@ class DockerEngine(ContainerEngine): ports=None, publish_all_ports=False, remove=False, - volumes=None + volumes=None, + **kwargs, ): container = self._client.containers.run( image_spec, @@ -107,5 +110,6 @@ class DockerEngine(ContainerEngine): publish_all_ports=publish_all_ports, remove=remove, volumes=(volumes or {}), + **kwargs, ) return DockerContainer(container) MODIFY repo2docker/engine.py repo2docker/engine.py @@ -147,7 +147,8 @@ class ContainerEngine(LoggingConfigurable): custom_context=False, dockerfile="", fileobj=None, - path="" + path="", + **kwargs ): """ Build a container @@ -242,7 +243,8 @@ class ContainerEngine(LoggingConfigurable): ports={}, publish_all_ports=False, remove=False, - volumes={} + volumes={}, + **kwargs ): """ Run a container

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Docker: print helpful message if daemon not running

MODIFY repo2docker/docker.py repo2docker/docker.py @@ -47,9 +47,8 @@ class DockerEngine(ContainerEngine): self._apiclient = docker.APIClient( version="auto", **docker.utils.kwargs_from_env() ) - self._client = docker.from_env(version="auto") except docker.errors.DockerException as e: - raise ContainerEngineException(e) + raise ContainerEngineException("Check if docker is running on the host.", e) def build( self, @@ -101,7 +100,8 @@ class DockerEngine(ContainerEngine): volumes=None, **kwargs, ): - container = self._client.containers.run( + client = docker.from_env(version="auto") + container = client.containers.run( image_spec, command=command, environment=(environment or []),

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Python 3.5: can't have trailing , in function arg list (again)

MODIFY repo2docker/docker.py repo2docker/docker.py @@ -61,7 +61,10 @@ class DockerEngine(ContainerEngine): dockerfile="", fileobj=None, path="", - **kwargs, + # fmt: off + # black adds a trailing , but this is invalid in Python 3.5 + **kwargs + # fmt: on ): return self._apiclient.build( buildargs=buildargs, @@ -98,7 +101,10 @@ class DockerEngine(ContainerEngine): publish_all_ports=False, remove=False, volumes=None, - **kwargs, + # fmt: off + # black adds a trailing , but this is invalid in Python 3.5 + **kwargs + # fmt: on ): client = docker.from_env(version="auto") container = client.containers.run(

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describe ContainerEngine volume and port formats

MODIFY repo2docker/engine.py repo2docker/engine.py @@ -80,7 +80,8 @@ class Container(ABC): str : The status of the container. Values include `created` `running` `exited`. - TODO: Does Docker have a fixed list of these? + Full list of statuses: + https://github.com/moby/moby/blob/v19.03.5/api/swagger.yaml#L4832 """ @@ -182,12 +183,10 @@ class ContainerEngine(LoggingConfigurable): custom_context : bool If `True` fileobj is a Tar file object containing the build context - TODO: Specific to Docker dockerfile : str Path to Dockerfile within the build context fileobj : tarfile A tar file-like object containing the build context - TODO: Specific to Docker, other clients can untar this to a tempdir path : str path to the Dockerfile @@ -270,15 +269,14 @@ class ContainerEngine(LoggingConfigurable): environment : list[str] List of environment variables in the form `ENVVAR=value` ports : dict - Container port bindings in the format expected by the engine - TODO: Should we use a fixed format and convert to whatever's required by the engine? + Container port bindings in the form generated by `repo2docker.utils.validate_and_generate_port_mapping` + https://github.com/jupyter/repo2docker/blob/0.11.0/repo2docker/utils.py#L95 publish_all_ports : bool If `True` publish all ports to host remove : bool If `True` delete container when it completes volumes : dict - Volume bindings in the format expected by the engine - TODO: Should we use a fixed format and convert to whatever's required by the engine? + Volume bindings in the form `{src : dest}` Returns -------

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