narySt/CommitChronicle_valPretrained · Datasets at Hugging Face

bump xeus-cling in tests so we don't have an old env relying on the free channel

MODIFY tests/external/reproductions.repos.yaml tests/external/reproductions.repos.yaml # get blocked by pinning - name: Xeus-Cling url: https://github.com/QuantStack/xeus-cling - ref: 0.4.5 + ref: 0.6.0 verify: jupyter kernelspec list # Zenodo record of https://github.com/binder-examples/requirements - name: 10.5281/zenodo.3242074

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comment about multiple json events per chunk

MODIFY repo2docker/app.py repo2docker/app.py @@ -457,6 +457,8 @@ class Repo2Docker(Application): layers = {} last_emit_time = time.time() for chunk in client.push(self.output_image_spec, stream=True): + # each chunk can be one or more lines of json events + # split lines here in case multiple are delivered at once for line in chunk.splitlines(): line = line.decode("utf-8", errors="replace") try: @@ -478,11 +480,10 @@ class Repo2Docker(Application): layers[progress["id"]] = progress if time.time() - last_emit_time > 1.5: self.log.info( - "Pushing image\n", extra=dict( - progress=progress_layers, - layers=layers, - phase="pushing", - ) + "Pushing image\n", + extra=dict( + progress=progress_layers, layers=layers, phase="pushing" + ), ) last_emit_time = time.time() self.log.info(

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Adding bash to Dockerfile to fix git-credential-env

MODIFY Dockerfile Dockerfile @@ -12,8 +12,8 @@ RUN mkdir /tmp/wheelhouse \ FROM alpine:${ALPINE_VERSION} -# install python, git -RUN apk add --no-cache git git-lfs python3 +# install python, git, bash +RUN apk add --no-cache git git-lfs python3 bash # install repo2docker COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse

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Make sure all loops over dict items are deterministic

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -90,7 +90,7 @@ 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.items() %} +{% for src, dst in build_script_files|dictsort %} COPY {{ src }} {{ dst }} {% endfor -%} {% endif -%} @@ -127,7 +127,7 @@ ENV {{item[0]}} {{item[1]}} # example installing APT packages. {% if preassemble_script_files -%} # If scripts required during build are present, copy them -{% for src, dst in preassemble_script_files.items() %} +{% for src, dst in preassemble_script_files|dictsort %} COPY src/{{ src }} ${REPO_DIR}/{{ dst }} {% endfor -%} {% endif -%} @@ -151,7 +151,7 @@ RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} # Container image Labels! # Put these at the end, since we don't want to rebuild everything # when these change! Did I mention I hate Dockerfile cache semantics? -{% for k, v in labels.items() %} +{% for k, v in labels|dictsort %} LABEL {{k}}="{{v}}" {%- endfor %}

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add assemble_subset get_assemble_files() returns list of files needed for assembly if buildpack.assemble_with_subset is set, only load assemble_files prior to running assembly scripts. Load the rest of the repo afterward conda opts in to this, but currently I think this works for everything *except* requirements.txt

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -178,6 +178,18 @@ class CondaBuildPack(BaseImage): """Am I building a Python 2 kernel environment?""" return self.python_version and self.python_version.split(".")[0] == "2" + def get_assemble_files(self): + """Specify that assembly only requires environment.yml + + enables caching assembly result even when + repo contents change + """ + assemble_files = super().get_assemble_files() + environment_yml = self.binder_path('environment.yml') + if os.path.exists(environment_yml): + assemble_files.append(environment_yml) + return assemble_files + def get_assemble_scripts(self): """Return series of build-steps specific to this source repository. """

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move stencila to preassemble

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -711,12 +711,8 @@ class BaseImage(BuildPack): except FileNotFoundError: pass - return scripts - - def get_assemble_scripts(self): - assemble_scripts = [] if "py" in self.stencila_contexts: - assemble_scripts.extend( + scripts.extend( [ ( "${NB_USER}", @@ -728,7 +724,7 @@ class BaseImage(BuildPack): ] ) if self.stencila_manifest_dir: - assemble_scripts.extend( + scripts.extend( [ ( "${NB_USER}", @@ -741,7 +737,11 @@ class BaseImage(BuildPack): ) ] ) - return assemble_scripts + return scripts + + def get_assemble_scripts(self): + """Return directives to run after the entire repository has been added to the image""" + return [] def get_post_build_scripts(self): post_build = self.binder_path("postBuild")

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conda install occurs in preassemble

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -178,19 +178,19 @@ class CondaBuildPack(BaseImage): """Am I building a Python 2 kernel environment?""" return self.python_version and self.python_version.split(".")[0] == "2" - def get_assemble_files(self): - """Specify that assembly only requires environment.yml + def get_preassemble_script_files(self): + """preassembly only requires environment.yml enables caching assembly result even when repo contents change """ - assemble_files = super().get_assemble_files() - environment_yml = self.binder_path('environment.yml') + assemble_files = super().get_preassemble_script_files() + environment_yml = self.binder_path("environment.yml") if os.path.exists(environment_yml): - assemble_files.append(environment_yml) + assemble_files[environment_yml] = environment_yml return assemble_files - def get_assemble_scripts(self): + def get_preassemble_scripts(self): """Return series of build-steps specific to this source repository. """ assembly_scripts = [] @@ -209,7 +209,7 @@ class CondaBuildPack(BaseImage): ), ) ) - return super().get_assemble_scripts() + assembly_scripts + return super().get_preassemble_scripts() + assembly_scripts def detect(self): """Check if current repo should be built with the Conda BuildPack.

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preassembly for pipfiles

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -65,7 +65,16 @@ class PipfileBuildPack(CondaBuildPack): self._python_version = self.major_pythons["3"] return self._python_version - def get_assemble_scripts(self): + def get_preassemble_script_files(self): + """Return files needed for preassembly""" + files = super().get_preassemble_script_files() + for name in ("requirements3.txt", "Pipfile", "Pipfile.lock"): + path = self.binder_path(name) + if os.path.exists(path): + files[path] = path + return files + + def get_preassemble_scripts(self): """Return series of build-steps specific to this repository. """ # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the

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set permissions on repo_dir prior to preassemble

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -132,6 +132,10 @@ COPY src/{{ src }} ${REPO_DIR}/{{ dst }} {% endfor -%} {% endif -%} +{% if preassemble_script_directives -%} +RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} +{% endif -%} + {% for sd in preassemble_script_directives -%} {{ sd }} {% endfor %}

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test local pip requirements

MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -110,3 +110,20 @@ def test_normalize_doi(): assert utils.normalize_doi("http://doi.org/10.1234/jshd123") == "10.1234/jshd123" assert utils.normalize_doi("https://doi.org/10.1234/jshd123") == "10.1234/jshd123" assert utils.normalize_doi("http://dx.doi.org/10.1234/jshd123") == "10.1234/jshd123" + + +@pytest.mark.parametrize( + "req, is_local", + [ + ("-r requirements.txt", True), + ("-e .", True), + ("file://subdir", True), + ("file://./subdir", True), + ("git://github.com/jupyter/repo2docker", False), + ("git+https://github.com/jupyter/repo2docker", False), + ("numpy", False), + ("# -e .", False), + ], +) +def test_local_pip_requirement(req, is_local): + assert utils.is_local_pip_requirement(req) == is_local

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typo in doi regexp must use `r` prefix when there are escapes

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -415,7 +415,7 @@ def deep_get(dikt, path): # Copyright (C) 2018 Alan Rubin. # Licensed under BSD-3-Clause license doi_regexp = re.compile( - "(doi:\s*|(?:https?://)?(?:dx\.)?doi\.org/)?(10\.\d+(.\d+)*/.+)$", flags=re.I + r"(doi:\s*|(?:https?://)?(?:dx\.)?doi\.org/)?(10\.\d+(.\d+)*/.+)$", flags=re.I )

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only install pipenv in preassemble save preassembly of pipenv for a later patch

MODIFY repo2docker/buildpacks/pipfile/__init__.py repo2docker/buildpacks/pipfile/__init__.py @@ -75,6 +75,15 @@ class PipfileBuildPack(CondaBuildPack): return files def get_preassemble_scripts(self): + """scripts to run prior to staging the repo contents""" + scripts = super().get_preassemble_scripts() + # install pipenv to install dependencies within Pipfile.lock or Pipfile + scripts.append( + ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26") + ) + return scripts + + def get_assemble_scripts(self): """Return series of build-steps specific to this repository. """ # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the @@ -113,11 +122,6 @@ class PipfileBuildPack(CondaBuildPack): # my_package_example = {path=".", editable=true} working_directory = self.binder_dir or "." - # install pipenv to install dependencies within Pipfile.lock or Pipfile - assemble_scripts.append( - ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26") - ) - # NOTES: # - Without prioritizing the PATH to KERNEL_PYTHON_PREFIX over # NB_SERVER_PYTHON_PREFIX, 'pipenv' draws the wrong conclusion about

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Update repo2docker/buildpacks/conda/__init__.py

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -145,7 +145,7 @@ class CondaBuildPack(BaseImage): # check if the env file is empty, if so instantiate an empty dictionary. if env is None: env = {} - # check if the env file provided a dick-like thing not a list or other data structure. + # check if the env file provided a dict-like thing not a list or other data structure. if not isinstance(env, Mapping): raise TypeError( "environment.yml should contain a dictionary. Got %r" % type(env)

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Call parent preassemble scripts methods Without this we don't collect the files that other build packs need to copy them over to the container in the pre-assemble stage.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -292,7 +292,7 @@ class RBuildPack(PythonBuildPack): return super().get_build_scripts() + scripts def get_preassemble_script_files(self): - files = {} + files = super().get_preassemble_script_files() installR_path = self.binder_path("install.R") if os.path.exists(installR_path): files[installR_path] = installR_path

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Add test for R buildpack's get_preassemble_script_files

ADD tests/unit/test_preassemble.py +import os + +import pytest + +from repo2docker import buildpacks + + +@pytest.mark.parametrize("binder_dir", ["", ".binder", "binder"]) +def test_combine_preassemble_steps(tmpdir, binder_dir): + tmpdir.chdir() + if binder_dir: + os.mkdir(binder_dir) + + # create two empty files for the build pack to use for pre-assembly + open(os.path.join(binder_dir, "requirements.txt"), "w").close() + open(os.path.join(binder_dir, "install.R"), "w").close() + + # trigger R build pack detection + with open(os.path.join(binder_dir, "runtime.txt"), "w") as f: + f.write("r-2019-01-30") + + bp = buildpacks.RBuildPack() + files = bp.get_preassemble_script_files() + + assert len(files) == 2 + assert os.path.join(binder_dir, "requirements.txt") in files + assert os.path.join(binder_dir, "install.R") in files

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switched pip packages to conda-forge

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -4,6 +4,5 @@ dependencies: - jupyterlab==0.35.4 - nbconvert==5.4.1 - notebook==5.7.8 - - pip: - - nteract_on_jupyter==2.0.12 - - jupyterhub==1.0.* + - jupyterhub=1.0.* + - nteract_on_jupyter=2.0.12

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clarify application of environment.yml

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -32,10 +32,10 @@ Below is a list of supported configuration files (roughly in the order of build ``environment.yml`` is the standard configuration file used by `conda <https://conda.io>`_ that lets you install any kind of package, including Python, R, and C/C++ packages. -``repo2docker`` does not use ``environment.yml`` to create and activate a new conda environment. -Rather, it updates a base conda environment with the packages listed in ``environment.yml``. +``repo2docker`` does not use your ``environment.yml`` to create and activate a new conda environment. +Rather, it updates a base conda environment `defined here <https://github.com/jupyter/repo2docker/blob/master/repo2docker/buildpacks/conda/environment.yml>`_ with the packages listed in your ``environment.yml``. This means that the environment will always have the same default name, not the name -specified in ``environment.yml``. +specified in your ``environment.yml``. .. note::

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node test for system package and conda-forge

MODIFY tests/base/node10/verify tests/base/node10/verify #!/bin/sh set -e +# check node from conda-forge which node node --version -node --version | grep v10 +node --version | grep v11 +# check node system package +/usr/bin/node --version +/usr/bin/node --version | grep v10 which npm npm --version

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Tiny typo in docs/source/index.rst

MODIFY docs/source/index.rst docs/source/index.rst @@ -6,7 +6,7 @@ images from source code repositories**. ``repo2docker`` fetches a repository (from GitHub, GitLab, Zenodo, a Git repository or a local directory) -and builds a container image inn which the code can be executed. +and builds a container image in which the code can be executed. The image build process is based on the configuration files found in the repository. ``repo2docker`` can be

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add hydroshare as a content provider

MODIFY repo2docker/app.py repo2docker/app.py @@ -142,7 +142,7 @@ class Repo2Docker(Application): # detecting if something will successfully `git clone` is very hard if all # you can do is look at the path/URL to it. content_providers = List( - [contentproviders.Local, contentproviders.Zenodo, contentproviders.Git], + [contentproviders.Local, contentproviders.Zenodo, contentproviders.Hydroshare, contentproviders.Git], config=True, help=""" Ordered list by priority of ContentProviders to try in turn to fetch

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use request.urlretrieve

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py -import urllib import zipfile -from urllib.request import urlopen, Request +from urllib.request import urlopen, Request, urlretrieve from urllib.error import HTTPError from .base import ContentProvider @@ -67,7 +66,7 @@ class Hydroshare(ContentProvider): yield "Fetching HydroShare Resource {}.\n".format(resource_id) bag_url = "{}{}".format(host["django_irods"], resource_id) - filehandle, _ = urllib.urlretrieve(bag_url) + filehandle, _ = urlretrieve(bag_url) zip_file_object = zipfile.ZipFile(filehandle, 'r') zip_file_object.extractall(output_dir)

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only use data/contents directory

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py import zipfile +import os +import shutil from urllib.request import urlopen, Request, urlretrieve from urllib.error import HTTPError @@ -55,7 +57,7 @@ class Hydroshare(ContentProvider): for host in hosts: if any([url.startswith(s) for s in host["hostname"]]): - self.resource_id = url.rsplit("/", maxsplit=1)[1] + self.resource_id = url.rsplit("/", maxsplit=2)[1] return {"resource": self.resource_id, "host": host} def fetch(self, spec, output_dir, yield_output=False): @@ -68,7 +70,12 @@ class Hydroshare(ContentProvider): bag_url = "{}{}".format(host["django_irods"], resource_id) filehandle, _ = urlretrieve(bag_url) zip_file_object = zipfile.ZipFile(filehandle, 'r') - zip_file_object.extractall(output_dir) + + zip_file_object.extractall("temp") + files = os.listdir(os.path.join("temp", self.resource_id, "data", "contents")) + for f in files: + shutil.move("temp" + f, output_dir) + shutil.rmtree("temp") @property def content_id(self):

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extract from contents directory

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -72,9 +72,10 @@ class Hydroshare(ContentProvider): zip_file_object = zipfile.ZipFile(filehandle, 'r') zip_file_object.extractall("temp") - files = os.listdir(os.path.join("temp", self.resource_id, "data", "contents")) + contents_dir = os.path.join("temp", self.resource_id, "data", "contents") + files = os.listdir(contents_dir) for f in files: - shutil.move("temp" + f, output_dir) + shutil.move(os.path.join(contents_dir, f), output_dir) shutil.rmtree("temp") @property

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handle traliing slash in url

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -57,7 +57,7 @@ class Hydroshare(ContentProvider): for host in hosts: if any([url.startswith(s) for s in host["hostname"]]): - self.resource_id = url.rsplit("/", maxsplit=2)[1] + self.resource_id = url.strip("/").rsplit("/", maxsplit=1)[1] return {"resource": self.resource_id, "host": host} def fetch(self, spec, output_dir, yield_output=False):

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allow for bag creation

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py import zipfile import os import shutil +import time from urllib.request import urlopen, Request, urlretrieve from urllib.error import HTTPError @@ -68,10 +69,21 @@ class Hydroshare(ContentProvider): yield "Fetching HydroShare Resource {}.\n".format(resource_id) bag_url = "{}{}".format(host["django_irods"], resource_id) + + # bag downloads are prepared on demand and may need some time + conn = urlopen(bag_url) + while str(conn.info().get_content_type()) != "application/zip": + if conn.getcode() != 200: + yield "Failed to download bag. status code {}".format(conn.getcode()) + return + yield "Bag is being prepared, requesting again in 3 seconds" + time.sleep(3) + filehandle, _ = urlretrieve(bag_url) zip_file_object = zipfile.ZipFile(filehandle, 'r') zip_file_object.extractall("temp") + # resources store the contents in the data/contents directory, which is all we want to keep contents_dir = os.path.join("temp", self.resource_id, "data", "contents") files = os.listdir(contents_dir) for f in files:

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actually reconnect

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -72,12 +72,13 @@ class Hydroshare(ContentProvider): # bag downloads are prepared on demand and may need some time conn = urlopen(bag_url) - while str(conn.info().get_content_type()) != "application/zip": + while conn.info().get_content_type() != "application/zip": if conn.getcode() != 200: yield "Failed to download bag. status code {}".format(conn.getcode()) return yield "Bag is being prepared, requesting again in 3 seconds" time.sleep(3) + conn = urlopen(bag_url) filehandle, _ = urlretrieve(bag_url) zip_file_object = zipfile.ZipFile(filehandle, 'r')

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extend wait time and cleanup messaging

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -74,10 +74,11 @@ class Hydroshare(ContentProvider): conn = urlopen(bag_url) while conn.info().get_content_type() != "application/zip": if conn.getcode() != 200: - yield "Failed to download bag. status code {}".format(conn.getcode()) + yield "Failed to download bag. status code {}.\n".format(conn.getcode()) return - yield "Bag is being prepared, requesting again in 3 seconds" - time.sleep(3) + wait_time = 10 + yield "Bag is being prepared, requesting again in {} seconds.\n".format(wait_time) + time.sleep(wait_time) conn = urlopen(bag_url) filehandle, _ = urlretrieve(bag_url)

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Upgrade IRKernel version to 1.0.2

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -174,7 +174,7 @@ class RBuildPack(PythonBuildPack): devtools_version = "2018-02-01" # IRKernel version - specified as a tag in the IRKernel repository - irkernel_version = "0.8.11" + irkernel_version = "1.0.2" mran_url = "https://mran.microsoft.com/snapshot/{}".format( self.checkpoint_date.isoformat()

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SUpport R runtime strings that don't specify a version

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -63,8 +63,9 @@ class RBuildPack(PythonBuildPack): version if found. """ if not hasattr(self, "_r_version"): - if self._runtime.startswith("r-"): - _, self._r_version, _ = self._runtime.split("-", 2) + parts = self.runtime.split("-") + if len(parts) == 5: + self._r_version = parts[1] else: self._r_version = ""

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avoid dirty in repo2docker version in docker image by calling git clean

MODIFY Dockerfile Dockerfile @@ -5,10 +5,12 @@ RUN apk add --no-cache git python3 python3-dev # build wheels in first image ADD . /tmp/src +RUN cd /tmp/src && git clean -xfd && git status RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ - && pip3 wheel --no-cache-dir /tmp/src + && pip3 wheel --no-cache-dir /tmp/src \ + && ls -l /tmp/wheelhouse FROM alpine:${ALPINE_VERSION} @@ -17,7 +19,8 @@ RUN apk add --no-cache git git-lfs python3 bash # install repo2docker COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse -RUN pip3 install --no-cache-dir /tmp/wheelhouse/*.whl +RUN pip3 install --no-cache-dir /tmp/wheelhouse/*.whl \ + && pip3 list # add git-credential helper COPY ./docker/git-credential-env /usr/local/bin/git-credential-env

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use repo2docker version in docker tags docker tags will include versioneer tag, e.g. `0.10.0-4.abc123` where 0.10.0 is the latest tag 4 is the number of commits since then abc123 is the current commit hash

MODIFY hooks/post_push hooks/post_push #!/bin/bash -# when building jupyter/repo2docker:master also push jupyter/repo2docker:abcd1234 - -HASH_IMAGE="$DOCKER_REPO:${SOURCE_COMMIT:0:8}" -docker tag $DOCKER_REPO:$DOCKER_TAG $HASH_IMAGE -docker push $HASH_IMAGE +# when building jupyter/repo2docker:master +# also push jupyter/repo2docker:1.2.3-3.abcd1234 (replace + with -) +version=$(docker run $DOCKER_REPO:$DOCKER_TAG jupyter-repo2docker --version | sed s@+@-@) +VERSION_IMAGE="$DOCKER_REPO:$version" +docker tag $DOCKER_REPO:$DOCKER_TAG "$VERSION_IMAGE" +docker push "$VERSION_IMAGE"

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Use new way of installing bioconductor

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -340,6 +340,8 @@ class RBuildPack(PythonBuildPack): ] if "r" in self.stencila_contexts: + # new versions of R require a different way of installing bioconductor + if self.r_version.startswith("3.4"): scripts += [ ( "${NB_USER}", @@ -352,6 +354,19 @@ class RBuildPack(PythonBuildPack): ) ] + else: + scripts += [ + ( + "${NB_USER}", + # Install and register stencila library + r""" + R --quiet -e "install.packages('BiocManager'); BiocManager::install(); BiocManager::install(c('graph'))" && \ + R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \ + R --quiet -e "stencila::register()" + """, + ) + ] + return super().get_build_scripts() + scripts def get_preassemble_script_files(self):

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let black have its way

MODIFY repo2docker/__main__.py repo2docker/__main__.py @@ -177,17 +177,9 @@ def get_argparser(): argparser.add_argument("--target-repo-dir", help=Repo2Docker.target_repo_dir.help) - argparser.add_argument( - "--appendix", - type=str, - help=Repo2Docker.appendix.help, - ) + argparser.add_argument("--appendix", type=str, help=Repo2Docker.appendix.help) - argparser.add_argument( - "--subdir", - type=str, - help=Repo2Docker.subdir.help, - ) + argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help) argparser.add_argument( "--version", @@ -197,10 +189,7 @@ def get_argparser(): ) argparser.add_argument( - '--cache-from', - action='append', - default=[], - help=Repo2Docker.cache_from.help, + "--cache-from", action="append", default=[], help=Repo2Docker.cache_from.help ) return argparser

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print Dockerfile to stdout when `--no-build` Removes need to also specify `--debug` to see the dockerfile, which goes to the logs

MODIFY repo2docker/app.py repo2docker/app.py @@ -686,7 +686,9 @@ class Repo2Docker(Application): self.log.debug(picked_buildpack.render(), extra=dict(phase="building")) - if not self.dry_run: + if self.dry_run: + print(picked_buildpack.render()) + else: if self.user_id == 0: raise ValueError( "Root as the primary user in the image is not permitted."

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respect self.log_level with json logs

MODIFY repo2docker/app.py repo2docker/app.py @@ -433,7 +433,7 @@ class Repo2Docker(Application): self.log = logging.getLogger("repo2docker") self.log.handlers = [] self.log.addHandler(logHandler) - self.log.setLevel(logging.INFO) + self.log.setLevel(self.log_level) else: # due to json logger stuff above, # our log messages include carriage returns, newlines, etc.

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only log Dockerfile at debug-level if not dry_run avoids double-display when using --debug --no-build

MODIFY repo2docker/app.py repo2docker/app.py @@ -684,11 +684,12 @@ class Repo2Docker(Application): picked_buildpack.labels["repo2docker.repo"] = repo_label picked_buildpack.labels["repo2docker.ref"] = self.ref - self.log.debug(picked_buildpack.render(), extra=dict(phase="building")) - if self.dry_run: print(picked_buildpack.render()) else: + self.log.debug( + picked_buildpack.render(), extra=dict(phase="building") + ) if self.user_id == 0: raise ValueError( "Root as the primary user in the image is not permitted."

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Add azure pipelines for testing

ADD azure-pipelines.yml +# https://docs.microsoft.com/azure/devops/pipelines/ecosystems/python +pool: + vmImage: "ubuntu-16.04" + +steps: +- task: UsePythonVersion@0 + inputs: + versionSpec: '3.6' + +- script: python -m pip install --upgrade pip setuptools wheel + displayName: 'Install tools' + +- script: pip install -r dev-requirements.txt + displayName: 'Install dev requirements' + +- script: pip install -e . + displayName: 'Install r2d' + +- script: pytest --durations 10 --cov repo2docker -v tests + displayName: 'Run pytest' MODIFY dev-requirements.txt dev-requirements.txt @@ -5,3 +5,4 @@ pytest>=3.6 wheel pytest-cov pre-commit +requests

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Add azure pipelines badge

MODIFY README.md README.md [![Build Status](https://travis-ci.org/jupyter/repo2docker.svg?branch=master)](https://travis-ci.org/jupyter/repo2docker) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) +[![Build Status](https://dev.azure.com/jupyter/repo2docker/_apis/build/status/jupyter.repo2docker?branchName=master)](https://dev.azure.com/jupyter/repo2docker/_build/latest?definitionId=1&branchName=master) `repo2docker` fetches a git repository and builds a container image based on the configuration files found in the repository.

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git needs to be set up

MODIFY azure-pipelines.yml azure-pipelines.yml @@ -7,6 +7,11 @@ steps: inputs: versionSpec: '3.6' +- script: | + git config --global user.email "ci@fake.tld" + git config --global user.name "CI Services" + displayName: 'Set up git' + - script: python -m pip install --upgrade pip setuptools wheel displayName: 'Install tools'

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Use LooseVersion to compare versions instead of strings

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -2,6 +2,8 @@ import re import os import datetime +from distutils.version import LooseVersion as V + from .python import PythonBuildPack @@ -170,7 +172,7 @@ class RBuildPack(PythonBuildPack): ] # For R 3.4 we use the default Ubuntu package, for other versions we # install from a different PPA - if self.r_version.startswith("3.4"): + if V(self.r_version) < V("3.5"): packages.append("r-base") return super().get_packages().union(packages) @@ -216,7 +218,7 @@ class RBuildPack(PythonBuildPack): scripts = [] # For R 3.4 we want to use the default Ubuntu package but otherwise # we use the packages from a PPA - if not self.r_version.startswith("3.4"): + if V(self.r_version) >= V("3.5"): scripts += [ ( "root", @@ -342,7 +344,7 @@ class RBuildPack(PythonBuildPack): if "r" in self.stencila_contexts: # new versions of R require a different way of installing bioconductor - if self.r_version.startswith("3.4"): + if V(self.r_version) <= V("3.5"): scripts += [ ( "${NB_USER}",

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Restore the hooks directory when building the docker image

MODIFY Dockerfile Dockerfile @@ -5,7 +5,8 @@ RUN apk add --no-cache git python3 python3-dev # build wheels in first image ADD . /tmp/src -RUN cd /tmp/src && git clean -xfd && git status +# restore the hooks directory so that the repository isn't marked as dirty +RUN cd /tmp/src && git clean -xfd && git checkout -- hooks && git status RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \

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add docs about building docs

MODIFY docs/source/contributing/contributing.md docs/source/contributing/contributing.md @@ -196,3 +196,16 @@ Server: ``` Then you are good to go! + +## Building the documentation locally + +If you only changed the documentation, you can also build the documentation locally using `sphinx` . + +```bash +#pip install -r docs/doc-requirements.txt + +cd docs/ +make html +``` + +Then open the file `docs/build/html/index.html` in your browser.

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add support for Figshare versions > 9

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""" MODIFY tests/unit/contentproviders/test_figshare.py tests/unit/contentproviders/test_figshare.py @@ -21,6 +21,17 @@ def test_content_id(): fig.detect("10.6084/m9.figshare.9782777") assert fig.content_id == "9782777" + fig.detect("10.6084/m9.figshare.9782777.v123") + assert fig.content_id == "9782777" + + +def test_content_version(): + with patch.object(Figshare, "urlopen") as fake_urlopen: + fake_urlopen.return_value.url = "https://figshare.com/articles/title/9782777/2" + fig = Figshare() + fig.detect("10.6084/m9.figshare.9782777.v2") + assert fig.content_version == "2" + test_fig = Figshare() test_fig.article_id = "123456"

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Add a command for generating dataverse data file

MODIFY setup.py setup.py +from distutils.cmd import Command from setuptools import setup, find_packages import sys import versioneer @@ -8,6 +9,35 @@ else: with open("README.md", encoding="utf8") as f: readme = f.read() + +class GenerateDataverseInstallationsFileCommand(Command): + description = "Generate Dataverse installations data map" + user_options = [] + + def initialize_options(self): + self.url = ( + "https://services.dataverse.harvard.edu/miniverse/map/installations-json" + ) + + def finalize_options(self): + pass + + def run(self): + from urllib.request import urlopen + import json + + resp = urlopen(self.url, timeout=5) + resp_body = resp.read() + data = json.loads(resp_body.decode("utf-8")) + if "installations" not in data: + raise ValueError("Malformed installation map.") + with open("repo2docker/contentproviders/dataverse.json", "wb") as fp: + fp.write(resp_body) + + +__cmdclass = versioneer.get_cmdclass() +__cmdclass["generate_dataverse_file"] = GenerateDataverseInstallationsFileCommand + setup( name="jupyter-repo2docker", version=versioneer.get_version(), @@ -48,7 +78,7 @@ setup( ], packages=find_packages(), include_package_data=True, - cmdclass=versioneer.get_cmdclass(), + cmdclass=__cmdclass, entry_points={ "console_scripts": [ "jupyter-repo2docker = repo2docker.__main__:main",

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Use the persistent id from the url regardless whether it's a DOI or not

MODIFY repo2docker/contentproviders/dataverse.py repo2docker/contentproviders/dataverse.py @@ -3,11 +3,11 @@ import json import shutil from urllib.request import Request -from urllib.parse import urlparse, urlunparse +from urllib.parse import urlparse, urlunparse, parse_qs from zipfile import ZipFile from .doi import DoiProvider -from ..utils import copytree, deep_get, is_doi, normalize_doi +from ..utils import copytree, deep_get class Dataverse(DoiProvider): @@ -42,6 +42,7 @@ class Dataverse(DoiProvider): # Parse the url, to get the base for later API calls parsed_url = urlparse(url) + query_args = parse_qs(parsed_url.query) # Corner case handling if parsed_url.path.startswith("/file.xhtml"): @@ -72,8 +73,11 @@ class Dataverse(DoiProvider): return self.record_id = deep_get(data, "items.0.dataset_persistent_id") - elif is_doi(doi): - self.record_id = "doi:" + normalize_doi(doi) + elif ( + parsed_url.path.startswith("/dataset.xhtml") + and "persistentId" in query_args + ): + self.record_id = deep_get(query_args, "persistentId.0") if hasattr(self, "record_id"): return {"record": self.record_id, "host": host} @@ -127,5 +131,5 @@ class Dataverse(DoiProvider): @property def content_id(self): - """The Dataverse persistent identifier (could use internal dataset_id too).""" + """The Dataverse persistent identifier.""" return self.record_id

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Use port 80 to download GPG keys to avoid firewall problems

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -230,10 +230,12 @@ class RBuildPack(PythonBuildPack): echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/r3.6-ubuntu.list """, ), + # Use port 80 to talk to the keyserver to increase the chances + # of being able to reach it from behind a firewall ( "root", r""" - apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 + apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 """, ), (

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fix _urlretrieve class method

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -32,7 +32,7 @@ class Hydroshare(DoiProvider): self.resource_id = url.strip("/").rsplit("/", maxsplit=1)[1] return {"resource": self.resource_id, "host": host} - def _urlretrieve(bag_url): + def _urlretrieve(self, bag_url): return urlretrieve(bag_url) def fetch(self, spec, output_dir, yield_output=False, timeout=120):

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update date parser to parse hydroshare date with timezone

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -3,6 +3,7 @@ import os import shutil import time import json +import dateutil.parser from urllib.request import urlopen, Request, urlretrieve from urllib.error import HTTPError @@ -36,8 +37,7 @@ class Hydroshare(DoiProvider): date = next( item for item in json_response["dates"] if item["type"] == "modified" )["start_date"] - date = date.split(".")[0] - return str(int(time.mktime(time.strptime(date, "%Y-%m-%dT%H:%M:%S")))) + return str(int(time.mktime(dateutil.parser.parse(date)))) url = self.doi2url(doi)

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use datetime for iso parsing

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -3,7 +3,7 @@ import os import shutil import time import json -import dateutil.parser +import datetime from urllib.request import urlopen, Request, urlretrieve from urllib.error import HTTPError @@ -37,7 +37,7 @@ class Hydroshare(DoiProvider): date = next( item for item in json_response["dates"] if item["type"] == "modified" )["start_date"] - return str(int(time.mktime(dateutil.parser.parse(date)))) + return datetime.strptime(date, "%Y-%m-%dT%H:%M:%S").timestamp() url = self.doi2url(doi)

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Bumped conda version to 4.7.12

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -4,7 +4,7 @@ set -ex cd $(dirname $0) MINICONDA_VERSION=4.7.10 -CONDA_VERSION=4.7.10 +CONDA_VERSION=4.7.12 # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ MD5SUM="1c945f2b3335c7b2b15130b1b2dc5cf4" MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,6 +5,6 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["conda", "--version"]).decode("utf8").strip() -assert out == "conda 4.7.10", out +assert out == "conda 4.7.12", out import numpy

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Updated RStudio Server and RStudio Shiny Server From official sites as shown: `# Via https`...

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -201,13 +201,12 @@ class RBuildPack(PythonBuildPack): We set the snapshot date used to install R libraries from based on the contents of runtime.txt. """ - # Latest version as of October 2, 2019 - rstudio_url = "https://download2.rstudio.org/rstudio-server-1.2.5001-amd64.deb" + # Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/ + rstudio_url = "https://download2.rstudio.org/server/trusty/amd64/rstudio-server-1.2.5001-amd64.deb" # This is MD5, because that is what RStudio download page provides! rstudio_checksum = "d77039693dd09c3ca48038aa74cd921a" # Via https://www.rstudio.com/products/shiny/download-server/ - # Latest version as of October 2, 2019 shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb" shiny_checksum = "9aeef6613e7f58f21c97a4600921340e"

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Restored Shiny Server version to its current v. As explained in discussion on the pull request (https://github.com/jupyter/repo2docker/pull/803#issuecomment-538013605), I restored the Shiny Server version to its current version on Binder, and thus only left RStudio being updated.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -207,8 +207,8 @@ class RBuildPack(PythonBuildPack): rstudio_checksum = "d33881b9ab786c09556c410e7dc477de" # Via https://www.rstudio.com/products/shiny/download-server/ - shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb" - shiny_checksum = "9aeef6613e7f58f21c97a4600921340e" + shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb" + shiny_checksum = "78371a8361ba0e7fec44edd2b8e425ac" # Version of MRAN to pull devtools from. devtools_version = "2018-02-01"

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Restored RStudio Server version to its current v. As explained in discussion on the pull request (comment)), I did the reverse of the last commit. I restored the RStudio Server version to its current version on Binder, and thus only left Shiny Server being updated.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -201,14 +201,15 @@ class RBuildPack(PythonBuildPack): We set the snapshot date used to install R libraries from based on the contents of runtime.txt. """ + # Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/ - rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb" + rstudio_url = "https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb" # This is MD5, because that is what RStudio download page provides! - rstudio_checksum = "d33881b9ab786c09556c410e7dc477de" + rstudio_checksum = "24cd11f0405d8372b4168fc9956e0386" # Via https://www.rstudio.com/products/shiny/download-server/ - shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb" - shiny_checksum = "78371a8361ba0e7fec44edd2b8e425ac" + shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb" + shiny_checksum = "9aeef6613e7f58f21c97a4600921340e" # Version of MRAN to pull devtools from. devtools_version = "2018-02-01"

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I tried my best to install r-base-dev I tried installing r-base-dev as it is advised in RStudio instructions. I did it adding this package wherever r-base was already.

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -40,6 +40,8 @@ class RBuildPack(PythonBuildPack): The `r-base` package from Ubuntu apt repositories is used to install R itself, rather than any of the methods from https://cran.r-project.org/. + + The `r-base-dev` package is installed as advised in RStudio instructions. """ @property @@ -177,7 +179,7 @@ class RBuildPack(PythonBuildPack): # For R 3.4 we use the default Ubuntu package, for other versions we # install from a different PPA if V(self.r_version) < V("3.5"): - packages.append("r-base") + packages.append("r-base", "r-base-dev") return super().get_packages().union(packages) @@ -245,6 +247,7 @@ class RBuildPack(PythonBuildPack): r""" apt-get update && \ apt-get install --yes r-base={} && \ + apt-get install --yes r-base-dev={} && \ apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/*

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Fixed packages.append and updated RStudio again

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -179,7 +179,8 @@ class RBuildPack(PythonBuildPack): # For R 3.4 we use the default Ubuntu package, for other versions we # install from a different PPA if V(self.r_version) < V("3.5"): - packages.append("r-base", "r-base-dev") + packages.append("r-base") + packages.append("r-base-dev") return super().get_packages().union(packages) @@ -205,9 +206,9 @@ class RBuildPack(PythonBuildPack): """ # Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/ - rstudio_url = "https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb" + rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb" # This is MD5, because that is what RStudio download page provides! - rstudio_checksum = "24cd11f0405d8372b4168fc9956e0386" + rstudio_checksum = "d33881b9ab786c09556c410e7dc477de" # Via https://www.rstudio.com/products/shiny/download-server/ shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"

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adduser: useradd --no-log-init to reduce lastlog size If the Docker host does not support sparse files /var/log/lastlog can be extremely large if a large UID is set. --no-log-init prevents lastlog being created.

MODIFY repo2docker/buildpacks/base.py repo2docker/buildpacks/base.py @@ -42,8 +42,15 @@ ARG NB_UID ENV USER ${NB_USER} ENV HOME /home/${NB_USER} -RUN adduser --disabled-password \ - --gecos "Default user" \ +RUN groupadd \ + --gid ${NB_UID} \ + ${NB_USER} && + useradd \ + --comment "Default user" \ + --create-home \ + --gid ${NB_UID} \ + --no-log-init \ + --shell /bin/bash \ --uid ${NB_UID} \ ${NB_USER}

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Added Tim's suggestions (link below)

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -248,13 +248,14 @@ class RBuildPack(PythonBuildPack): "root", r""" apt-get update && \ - apt-get install --yes r-base={} && \ - apt-get install --yes r-base-dev={} && \ + apt-get install --yes r-base={R_version} \ + r-base-dev={R_version} \ + libclang-dev && \ apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* """.format( - self.r_version + R_version=self.r_version ), ), ]

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update downloading message to include full url

MODIFY repo2docker/contentproviders/hydroshare.py repo2docker/contentproviders/hydroshare.py @@ -64,10 +64,10 @@ class Hydroshare(DoiProvider): resource_id = spec["resource"] host = spec["host"] - yield "Fetching HydroShare Resource {}.\n".format(resource_id) - bag_url = "{}{}".format(host["django_irods"], resource_id) + yield "Downloading {}.\n".format(bag_url) + # bag downloads are prepared on demand and may need some time conn = self.urlopen(bag_url) total_wait_time = 0

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Fix submodule check out

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -23,7 +23,12 @@ class Git(ContentProvider): try: cmd = ["git", "clone", "--recursive"] if ref is None: + # check out of HEAD is performed after the clone is complete cmd.extend(["--depth", "1"]) + else: + # don't check out HEAD, the given ref will be checked out later + # this prevents HEAD's submodules to be cloned if ref doesn't have them + cmd.extend(["--no-checkout"]) cmd.extend([repo, output_dir]) for line in execute_cmd(cmd, capture=yield_output): yield line @@ -34,6 +39,11 @@ class Git(ContentProvider): # check out the specific ref given by the user if ref is not None: + # check out ref as it has not been done yet + for line in execute_cmd( + ["git", "checkout", ref], cwd=output_dir, capture=yield_output + ): + yield line hash = check_ref(ref, output_dir) if hash is None: self.log.error(

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Add change description

MODIFY docs/source/changelog.rst docs/source/changelog.rst @@ -10,6 +10,7 @@ Release date: TBD New features ------------ +- Fix for submodule check out in :pr:`809` by :user:`davidbrochart`. - Add support for Figshare in :pr:`788` by :user:`nuest`. - Add support for Dataverse in :pr:`739` by :user:`Xarthisius`.

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Clone and check out branch in two steps

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -23,15 +23,18 @@ class Git(ContentProvider): try: cmd = ["git", "clone"] if ref is None: + # check out of HEAD is performed after the clone is complete cmd.extend(["--depth", "1"]) else: - cmd.extend(["--branch", ref]) + # don't check out HEAD, the given ref will be checked out later + # this prevents HEAD's submodules to be cloned if ref doesn't have them + cmd.extend(["--no-checkout"]) cmd.extend([repo, output_dir]) for line in execute_cmd(cmd, capture=yield_output): yield line except subprocess.CalledProcessError as e: - msg = "Failed to clone repository from {repo}".format(repo=repo) + msg = "Failed to clone repository from {repo}.".format(repo=repo) if ref is not None: msg += " (ref {ref})".format(ref=ref) msg += "." @@ -39,6 +42,15 @@ class Git(ContentProvider): # check out the specific ref given by the user if ref is not None: + # check out ref as it has not been done yet + try: + for line in execute_cmd( + ["git", "checkout", ref], cwd=output_dir, capture=yield_output + ): + yield line + except subprocess.CalledProcessError as e: + msg = "Failed to check out ref {ref}.".format(ref=ref) + raise ContentProviderException(msg) from e hash = check_ref(ref, output_dir) if hash is None: self.log.error(

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Raise ValueError if not able to checkout ref

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -42,21 +42,17 @@ class Git(ContentProvider): # check out the specific ref given by the user if ref is not None: - # check out ref as it has not been done yet - try: - for line in execute_cmd( - ["git", "checkout", ref], cwd=output_dir, capture=yield_output - ): - yield line - except subprocess.CalledProcessError as e: - msg = "Failed to check out ref {ref}.".format(ref=ref) - raise ContentProviderException(msg) from e hash = check_ref(ref, output_dir) if hash is None: self.log.error( "Failed to check out ref %s", ref, extra=dict(phase="failed") ) raise ValueError("Failed to check out ref {}".format(ref)) + # check out ref as it has not been done yet + for line in execute_cmd( + ["git", "checkout", ref], cwd=output_dir, capture=yield_output + ): + yield line # 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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Dot gets added later

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -34,7 +34,7 @@ class Git(ContentProvider): yield line except subprocess.CalledProcessError as e: - msg = "Failed to clone repository from {repo}.".format(repo=repo) + msg = "Failed to clone repository from {repo}".format(repo=repo) if ref is not None: msg += " (ref {ref})".format(ref=ref) msg += "."

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Check out hash, not ref

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -50,7 +50,7 @@ class Git(ContentProvider): raise ValueError("Failed to check out ref {}".format(ref)) # check out ref as it has not been done yet for line in execute_cmd( - ["git", "checkout", ref], cwd=output_dir, capture=yield_output + ["git", "checkout", hash], cwd=output_dir, capture=yield_output ): yield line # If the hash is resolved above, we should be able to reset to it

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Remove explicit checkout when ref given

MODIFY repo2docker/contentproviders/git.py repo2docker/contentproviders/git.py @@ -48,12 +48,9 @@ class Git(ContentProvider): "Failed to check out ref %s", ref, extra=dict(phase="failed") ) raise ValueError("Failed to check out ref {}".format(ref)) - # check out ref as it has not been done yet - for line in execute_cmd( - ["git", "checkout", hash], cwd=output_dir, capture=yield_output - ): - yield line - # If the hash is resolved above, we should be able to reset to it + # We don't need to explicitly checkout things as the reset will + # take 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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DOC: Fixes link rendering

MODIFY docs/source/faq.rst docs/source/faq.rst @@ -172,7 +172,7 @@ possible (this is why repo2docker buildpacks largely build off of patterns that exist in the data analytics community). We try to perform due-diligence and search for other communities to leverage and help, but sometimes it makes the most sense to build our own new tool. In the case of repo2docker, we spent time integrating with a pre-existing -tool called [source2image](https://github.com/openshift/source-to-image). +tool called `source2image <https://github.com/openshift/source-to-image/>`_. This is an excellent open tool for containerization, but we ultimately decided that it did not fit the use-case we wanted to address. For more information, -[here's a short blog post about the decision and the reasoning behind it](https://github.com/yuvipanda/words/blob/fd096dd49d87e624acd8bdf6d13c0cecb930bb3f/content/post/why-not-s2i.md). +`here <https://github.com/yuvipanda/words/blob/fd096dd49d87e624acd8bdf6d13c0cecb930bb3f/content/post/why-not-s2i.md>`_ is a short blog post about the decision and the reasoning behind it.

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updating config files to avoid links

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -17,12 +17,8 @@ GitHub contains a list of sample repositories for common configurations that ``repo2docker`` can build with various configuration files such as Python and R installation in a repository. -Below is a list of supported configuration files (roughly in the order of build priority): - -.. contents:: - :local: - :depth: 1 - +A list of supported configuration files (roughly in the order of build priority) +can be found on this page (and to the right). .. _environment.yml:

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adding short explainers for index pages

MODIFY docs/source/configuration/index.rst docs/source/configuration/index.rst Configuring your repository =========================== +Information about configuring your repository to work with repo2docker, +and controlling elements of the built environment using configuration files. + .. toctree:: :maxdepth: 2 :caption: Complete list of configuration files MODIFY docs/source/contributing/index.rst docs/source/contributing/index.rst Contributing ============ +The repo2docker community is welcoming of all kinds of help and +participation from others. Below are a few ways that you can get involved, +as well as resources for understanding the structure and design of the +repo2docker package. + .. toctree:: contributing MODIFY docs/source/getting-started/index.rst docs/source/getting-started/index.rst Getting Started =============== +Instructions and information on how to get started with repo2docker +on your own machine. Select from the pages listed below to begin. + .. toctree:: :maxdepth: 2 - :caption: Getting started with repo2docker ../install ../usage MODIFY docs/source/howto/index.rst docs/source/howto/index.rst @@ -3,6 +3,7 @@ How-to Guides ============= Short, actionable guides that cover specific topics with repo2docker. +Select from the pages listed below to get started. .. toctree:: :maxdepth: 2

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Fix a broken link, update favicon

MODIFY docs/source/_static/images/favicon.ico docs/source/_static/images/favicon.ico Binary files a/docs/source/_static/images/favicon.ico and b/docs/source/_static/images/favicon.ico differ MODIFY docs/source/design.md docs/source/design.md @@ -49,10 +49,8 @@ Many ingredients go into making an image from a repository: 1. versions of the libraries installed by the repository `repo2docker` controls the first two, the user controls the third one. The current -policy for the version of the base image is that we will keep pace with Ubuntu -releases until we reach the next release with Long Term Support (LTS). We -currently use Artful Aardvark (17.10) and the next LTS version will be -Bionic Beaver (18.04). +policy for the version of the base image is that we will use the current LTS +version Bionic Beaver (18.04) for the foreseeable future. The version of `repo2docker` used to build an image can influence which packages are installed by default and which features are supported during the build @@ -73,7 +71,7 @@ that's separated out cleanly. This allows easy use by other projects (like BinderHub). There is additional (and very useful) design advice on this in -the [Art of Unix Programming](http://www.faqs.org/docs/artu/ch01s06.html) which +the [Art of Unix Programming](https://web.archive.org/web/20190921131144/http://www.faqs.org/docs/artu/ch01s06.html) which is a highly recommended quick read. ## Composability

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r build-pack: when using ppa install r-recommended Attempt at fixing

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py @@ -250,6 +250,7 @@ class RBuildPack(PythonBuildPack): apt-get update && \ apt-get install --yes r-base={R_version} \ r-base-dev={R_version} \ + r-recommended={R_version} \ libclang-dev && \ apt-get -qq purge && \ apt-get -qq clean && \

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Remove a test of legacy buildpack

MODIFY tests/unit/test_cache_from.py tests/unit/test_cache_from.py @@ -50,23 +50,3 @@ def test_cache_from_docker(tmpdir): called_args, called_kwargs = fake_client.build.call_args assert "cache_from" in called_kwargs assert called_kwargs["cache_from"] == cache_from - - -def test_cache_from_legacy(tmpdir): - cache_from = ["image-1:latest"] - fake_log_value = {"stream": "fake"} - fake_client = MagicMock(spec=docker.APIClient) - fake_client.build.return_value = iter([fake_log_value]) - extra_build_kwargs = {"somekey": "somevalue"} - - # Test legacy docker image - with tmpdir.join("Dockerfile").open("w") as f: - f.write("FROM andrewosh/binder-base\n") - - for line in LegacyBinderDockerBuildPack().build( - fake_client, "image-2", 100, {}, cache_from, extra_build_kwargs - ): - assert line == fake_log_value - called_args, called_kwargs = fake_client.build.call_args - assert "cache_from" in called_kwargs - assert called_kwargs["cache_from"] == cache_from

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Replace deprecated with removed

MODIFY repo2docker/buildpacks/legacy/__init__.py repo2docker/buildpacks/legacy/__init__.py @@ -25,7 +25,7 @@ class LegacyBinderDockerBuildPack: if line.startswith("FROM"): if "andrewosh/binder-base" in line.split("#")[0].lower(): log.error( - "The legacy buildpack was deprecated in January 2020." + "The legacy buildpack was removed in January 2020." ) log.error( "Please see https://repo2docker.readthedocs.io/en/"

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Add contributor badge

MODIFY README.md README.md [![Build Status](https://travis-ci.org/jupyter/repo2docker.svg?branch=master)](https://travis-ci.org/jupyter/repo2docker) [![Documentation Status](https://readthedocs.org/projects/repo2docker/badge/?version=latest)](http://repo2docker.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://dev.azure.com/jupyter/repo2docker/_apis/build/status/jupyter.repo2docker?branchName=master)](https://dev.azure.com/jupyter/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 the configuration files found in the repository.

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Make sure the exit status gets passed along

MODIFY azure-pipelines.yml azure-pipelines.yml @@ -62,7 +62,7 @@ steps: - script: pip install -e . displayName: 'Install repo2docker' -- script: pushd tests; pytest --durations 10 --cov repo2docker -v $(REPO_TYPE); popd +- script: pushd tests && pytest --durations 10 --cov repo2docker -v $(REPO_TYPE) && popd displayName: 'Run tests $(REPO_TYPE)' - script: | MODIFY tests/unit/test_app.py tests/unit/test_app.py @@ -11,6 +11,10 @@ from repo2docker.__main__ import make_r2d from repo2docker.utils import chdir +def test_always_fails(): + assert False + + def test_find_image(): images = [{"RepoTags": ["some-org/some-repo:latest"]}]

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Remove "always fail" test

MODIFY tests/unit/test_app.py tests/unit/test_app.py @@ -11,10 +11,6 @@ from repo2docker.__main__ import make_r2d from repo2docker.utils import chdir -def test_always_fails(): - assert False - - def test_find_image(): images = [{"RepoTags": ["some-org/some-repo:latest"]}]

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use jupyterhub-base removes nodejs from the conda environment node is already installed on the host

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml @@ -2,7 +2,7 @@ dependencies: - python=3.7 - ipywidgets==7.4.2 - jupyterlab==0.35.4 - - jupyterhub=1.1.0 - nbconvert==5.4.1 - notebook==5.7.8 + - jupyterhub-base==1.1.0 - nteract_on_jupyter==2.1.3

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update node10 test to reflect the removal of conda nodejs

MODIFY tests/base/node10/verify tests/base/node10/verify #!/bin/sh -set -e -# check node from conda-forge +set -ex + +# check node system package and its version which node node --version -node --version | grep v11 -# check node system package -/usr/bin/node --version -/usr/bin/node --version | grep v10 +node --version | grep v10 which npm npm --version

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update base environment notebook 6 nbconvert 5.6 jupyterlab 1.2 widgets 7.5

MODIFY repo2docker/buildpacks/conda/environment.yml repo2docker/buildpacks/conda/environment.yml dependencies: - python=3.7 - - ipywidgets==7.4.2 - - jupyterlab==0.35.4 - - nbconvert==5.4.1 - - notebook==5.7.8 + - ipywidgets==7.5.1 + - jupyterlab==1.2.6 - jupyterhub-base==1.1.0 + - nbconvert==5.6.1 + - notebook==6.0.3 - nteract_on_jupyter==2.1.3

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Only check str dependencies

MODIFY repo2docker/buildpacks/conda/__init__.py repo2docker/buildpacks/conda/__init__.py @@ -237,7 +237,13 @@ class CondaBuildPack(BaseImage): """ if not hasattr(self, "_uses_r"): deps = self.environment_yaml.get("dependencies", []) - self._uses_r = any(dep.startswith("r-") for dep in deps) + self._uses_r = False + for dep in deps: + if not isinstance(dep, str): + continue + if dep.startswith("r-"): + self._uses_r = True + break return self._uses_r

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Add tests for r-in-conda

ADD tests/conda/r/environment.yml +dependencies: + - r-base=3.6 + - r-ggplot2 ADD tests/conda/r/verify +#!/bin/sh + +jupyter serverextension list 2>&1 | grep jupyter_server_proxy +jupyter nbextension list 2>&1 | grep jupyter_server_proxy +R -e "library('ggplot2')"

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use old Python environment when using old Julia environment

MODIFY repo2docker/buildpacks/julia/julia_require.py repo2docker/buildpacks/julia/julia_require.py """Generates a Dockerfile based on an input matrix with REQUIRE for legacy Julia""" + +from distutils.version import LooseVersion as V import os + from ..python import PythonBuildPack @@ -11,6 +14,16 @@ class JuliaRequireBuildPack(PythonBuildPack): minor_julias = {"0.6": "0.6.4", "0.7": "0.7.0", "1.0": "1.0.4", "1.1": "1.1.1"} major_julias = {"1": "1.1.1"} + @property + def python_version(self): + # IJulia doesn't build on julia 0.6 + # due to old incompatibilities with Jupyter-core >= 4.5, + # so use the similarly-old Python 3.5 base environment + if V(self.julia_version) < V("0.7"): + return "3.5" + else: + return super().python_version + @property def julia_version(self): require = self.binder_path("REQUIRE")

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bump miniconda version to 4.7.12

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -21,8 +21,8 @@ from ruamel.yaml import YAML # Docker image version can be different than conda version, # since miniconda3 docker images seem to lag conda releases. -MINICONDA_DOCKER_VERSION = "4.5.12" -CONDA_VERSION = "4.7.10" +MINICONDA_DOCKER_VERSION = "4.7.12" +CONDA_VERSION = "4.7.12" HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__))) MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash set -ex cd $(dirname $0) -MINICONDA_VERSION=4.7.10 +MINICONDA_VERSION=4.7.12.1 CONDA_VERSION=4.7.12 # Only MD5 checksums are available for miniconda # Can be obtained from https://repo.continuum.io/miniconda/ -MD5SUM="1c945f2b3335c7b2b15130b1b2dc5cf4" +MD5SUM="81c773ff87af5cfac79ab862942ab6b3" URL="https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniconda-installer.sh

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make conda install conda quick with -S if the version is already satisfied

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -76,7 +76,7 @@ def freeze(env_file, frozen_file): "; ".join( [ "set -ex", - f"conda install -yq conda={CONDA_VERSION}", + f"conda install -yq -S conda={CONDA_VERSION}", "conda config --add channels conda-forge", "conda config --system --set auto_update_conda false", f"conda env create -v -f /r2d/{env_file.relative_to(HERE)} -n r2d",

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add py3.8 to freeze list and remove 3.5 which is no longer being refrozen

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -119,7 +119,7 @@ def set_python(py_env_file, py): if __name__ == "__main__": # allow specifying which Pythons to update on argv - pys = sys.argv[1:] or ("2.7", "3.5", "3.6", "3.7") + pys = sys.argv[1:] or ("2.7", "3.6", "3.7", "3.8") for py in pys: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) set_python(env_file, py)

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make python 3.7 the default explicitly rather than implicit on the last entry

MODIFY repo2docker/buildpacks/conda/freeze.py repo2docker/buildpacks/conda/freeze.py @@ -6,7 +6,7 @@ It runs the freeze in a continuumio/miniconda3 image to ensure portability Usage: -python freeze.py [3.5] +python freeze.py [3.8] """ from datetime import datetime @@ -120,11 +120,11 @@ def set_python(py_env_file, py): if __name__ == "__main__": # allow specifying which Pythons to update on argv pys = sys.argv[1:] or ("2.7", "3.6", "3.7", "3.8") + default_py = "3.7" for py in pys: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) set_python(env_file, py) frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + ".frozen.yml") freeze(env_file, frozen_file) - - # use last version as default + if py == default_py: shutil.copy(frozen_file, FROZEN_FILE)

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docs: postBuild warn about shell script errors being ignored

MODIFY docs/source/config_files.rst docs/source/config_files.rst @@ -176,6 +176,9 @@ To see example repositories, visit our A script that can contain arbitrary commands to be run after the whole repository has been built. If you want this to be a shell script, make sure the first line is ``#!/bin/bash``. +Note that by default the build will not be stopped if an error occurs inside a shell script. +You should include ``set -e`` or the equivalent at the start of the script to avoid errors being silently ignored. + An example use-case of ``postBuild`` file is JupyterLab's demo on mybinder.org. It uses a ``postBuild`` file in a folder called ``binder`` to `prepare their demo for binder <https://github.com/jupyterlab/jupyterlab-demo/blob/master/binder/postBuild>`_.

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Install jupyter-offlinenotebook extension This adds the offlinenotebook extension to the base install. With this users can download their notebook even after the server has gone away.

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -50,6 +50,13 @@ echo "installing notebook env:" cat /tmp/environment.yml 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 +# and this installs it for lab +${NB_PYTHON_PREFIX}/bin/jupyter labextension install jupyter-offlinenotebook + # empty conda history file, # which seems to result in some effective pinning of packages in the initial env, # which we don't intend.

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Make it optional to install the extension for lab Some versions of lab used by repo2docker are not compatible with the offlinenotebook extension. We try to install the extension and if it fails we move on without raising an error.

MODIFY repo2docker/buildpacks/conda/install-miniconda.bash repo2docker/buildpacks/conda/install-miniconda.bash @@ -54,8 +54,9 @@ conda env create -p ${NB_PYTHON_PREFIX} -f /tmp/environment.yml # after the server connection has been lost # This will install and enable the extension for jupyter notebook ${NB_PYTHON_PREFIX}/bin/python -m pip install https://github.com/manics/jupyter-offlinenotebook/archive/7ba3520.zip -# and this installs it for lab -${NB_PYTHON_PREFIX}/bin/jupyter labextension install jupyter-offlinenotebook +# 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 # empty conda history file, # which seems to result in some effective pinning of packages in the initial env,

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utils.execute_cmd flush buffer if no EOL

MODIFY repo2docker/utils.py repo2docker/utils.py @@ -50,6 +50,8 @@ def execute_cmd(cmd, capture=False, **kwargs): if c == b"\n": yield flush() c_last = c + if buf: + yield flush() finally: ret = proc.wait() if ret != 0:

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If looking for latest MRAN URL try earlier snapshots too

MODIFY repo2docker/buildpacks/r.py repo2docker/buildpacks/r.py import re import os import datetime +import requests from distutils.version import LooseVersion as V @@ -135,8 +136,9 @@ class RBuildPack(PythonBuildPack): # no R snapshot date set through runtime.txt # set the R runtime to the latest date that is guaranteed to # be on MRAN across timezones - self._checkpoint_date = datetime.date.today() - datetime.timedelta( - days=2 + two_days_ago = datetime.date.today() - datetime.timedelta(days=2) + self._checkpoint_date = self._get_latest_working_mran_date( + two_days_ago, 3 ) self._runtime = "r-{}".format(str(self._checkpoint_date)) return True @@ -186,6 +188,29 @@ class RBuildPack(PythonBuildPack): return super().get_packages().union(packages) + def _get_latest_working_mran_date(self, startdate, max_prior): + """ + Look for a working MRAN snapshot + + Starts from `startdate` and tries up to `max_prior` previous days. + Raises `requests.HTTPError` with the last tried URL if no working snapshot found. + """ + for days in range(0, max_prior + 1): + test_date = startdate - datetime.timedelta(days=days) + mran_url = "https://mran.microsoft.com/snapshot/{}".format( + test_date.isoformat() + ) + r = requests.head(mran_url) + if r.ok: + return test_date + self.log.warning( + "Failed to get MRAN snapshot URL %s: %s %s", + mran_url, + r.status_code, + r.reason, + ) + r.raise_for_status() + def get_build_scripts(self): """ Return series of build-steps common to all R repositories

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unit test for utils.execute_cmd no EOL

MODIFY tests/unit/test_utils.py tests/unit/test_utils.py @@ -27,6 +27,14 @@ def test_capture_cmd_capture_success(): assert line == "test\n" +def test_capture_cmd_noeol_capture_success(): + # This should succeed + lines = list( + utils.execute_cmd(["/bin/bash", "-c", "echo -en 'test\ntest'"], capture=True) + ) + assert lines == ["test\n", "test"] + + def test_capture_cmd_capture_fail(): with pytest.raises(subprocess.CalledProcessError): for line in utils.execute_cmd(

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Replace reference to md5 with reference to sha256

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -20,7 +20,7 @@ chmod +x ${INSTALLER_PATH} # check sha256 checksum if ! echo "${SHA256SUM} ${INSTALLER_PATH}" | sha256sum --quiet -c -; then - echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!" + echo "sha256 mismatch for ${INSTALLER_PATH}, exiting!" exit 1 fi

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Fix conda test to account for newer conda

MODIFY tests/conda/binder-dir/verify tests/conda/binder-dir/verify @@ -5,6 +5,6 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["conda", "--version"]).decode("utf8").strip() -assert out == "conda 4.7.12", out +assert out == "conda 4.8.2", out import numpy

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Don't explicitly try to upgrade conda Unlike miniconda, miniforge is likely to be updated more often (one hopes), so we don't have to install then upgrade conda specifically

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -4,11 +4,10 @@ set -ex cd $(dirname $0) MINIFORGE_VERSION=4.8.2-1 -CONDA_VERSION=4.8.2 # SHA256 for installers can be obtained from https://github.com/conda-forge/miniforge/releases SHA256SUM="4f897e503bd0edfb277524ca5b6a5b14ad818b3198c2f07a36858b7d88c928db" -URL="https://github.com/conda-forge/miniforge/releases/download/4.8.2-1/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh" +URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/miniforge-installer.sh # make sure we don't do anything funky with user's $HOME @@ -34,14 +33,6 @@ conda config --system --set show_channel_urls true # bug in conda 4.3.>15 prevents --set update_dependencies echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc -# install conda itself, if needed -# FIXME: MINIFORGE_VERSION might have a build number, like -1. -# This will force conda to be installed each time -# Use a better way of finding conda version! -if [[ "${CONDA_VERSION}" != "${MINIFORGE_VERSION}" ]]; then - conda install -yq conda==${CONDA_VERSION} -fi - # avoid future changes to default channel_priority behavior conda config --system --set channel_priority "flexible"

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Add defaults channel back

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -26,6 +26,9 @@ fi bash ${INSTALLER_PATH} -b -p ${CONDA_DIR} export PATH="${CONDA_DIR}/bin:$PATH" +# Preserve behavior of miniconda - packages come from conda-forge + defaults +conda config --system --add channels defaults + # Do not attempt to auto update conda or dependencies conda config --system --set auto_update_conda false conda config --system --set show_channel_urls true

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Make defaults channel be lower priority than conda-forge

MODIFY repo2docker/buildpacks/conda/install-miniforge.bash repo2docker/buildpacks/conda/install-miniforge.bash @@ -27,7 +27,7 @@ bash ${INSTALLER_PATH} -b -p ${CONDA_DIR} export PATH="${CONDA_DIR}/bin:$PATH" # Preserve behavior of miniconda - packages come from conda-forge + defaults -conda config --system --add channels defaults +conda config --system --append channels defaults # Do not attempt to auto update conda or dependencies conda config --system --set auto_update_conda false

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Adopt new Sphinx theme name

MODIFY docs/doc-requirements.txt docs/doc-requirements.txt sphinx>=1.4, !=1.5.4 recommonmark sphinxcontrib-autoprogram -git+https://github.com/pandas-dev/pandas-sphinx-theme.git@master +pydata-sphinx-theme MODIFY docs/source/conf.py docs/source/conf.py @@ -117,7 +117,7 @@ html_favicon = "_static/images/favicon.ico" # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = "pandas_sphinx_theme" +html_theme = "pydata_sphinx_theme" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the

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Document loose conda export with --from-history

MODIFY docs/source/howto/export_environment.rst docs/source/howto/export_environment.rst @@ -26,6 +26,24 @@ be resolved (``ResolvePackageNotFound``). The solution ============ +Export your explicit install commands +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +If you only want to have an ``environment.yml`` that reflects the +``conda install`` you have run to build your conda environment, you can use +``conda env export --from-history environment.yml``. The resulting +``environment.yml`` then contains a loose pinning of the versions used, e.g. +``pandas=0.25`` if you explicitly requested this ``pandas`` version on +installation. If you didn't list a version constraint during installation, it +will also not be listed in your ``environment.yml``. + +While this approach doesn't lead to perfect reproducibilty, it will contain +just the same packages as if you would recreate the enviroment with the same +commands again today. + +Strict version export +~~~~~~~~~~~~~~~~~~~~~ + Follow this procedure to create a strict export of your environment that will work with ``repo2docker`` and sites like `mybinder.org <https://mybinder.org/>`_.

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MODIFY docs/source/howto/export_environment.rst docs/source/howto/export_environment.rst @@ -29,9 +29,10 @@ The solution Export your explicit install commands ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -If you only want to have an ``environment.yml`` that reflects the -``conda install`` you have run to build your conda environment, you can use -``conda env export --from-history environment.yml``. The resulting +To get a minimal ``environment.yml`` that only contains the packages you +explicitly installed run +``conda env export --from-history -f environment.yml``. We recommend that you +use this option to create your ``environment.yml``. The resulting ``environment.yml`` then contains a loose pinning of the versions used, e.g. ``pandas=0.25`` if you explicitly requested this ``pandas`` version on installation. If you didn't list a version constraint during installation, it

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Formatting changes only

MODIFY tests/unit/test_r.py tests/unit/test_r.py @@ -64,9 +64,7 @@ def test_mran_date(tmpdir, runtime, expected): assert r.checkpoint_date == date(*expected) -@pytest.mark.parametrize( - "expected", ["2019-12-29", "2019-12-26"], -) +@pytest.mark.parametrize("expected", ["2019-12-29", "2019-12-26"]) def test_mran_latestdate(tmpdir, expected): def mock_request_head(url): r = Response()

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