Merge branch 'master' into bump_ubuntu

Makefile

@@ -49,6 +49,9 @@ build/%: ## build the latest image for a stack
 build-all: $(foreach I,$(ALL_IMAGES),arch_patch/$(I) build/$(I) ) ## build all stacks
 build-test-all: $(foreach I,$(ALL_IMAGES),arch_patch/$(I) build/$(I) test/$(I) ) ## build and test all stacks
 
+check-outdated/%: ## check the outdated conda packages in a stack and produce a report (experimental)
+	@TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest test/test_outdated.py
+
 dev/%: ARGS?=
 dev/%: DARGS?=
 dev/%: PORT?=8888
@@ -89,4 +92,5 @@ tx-en: ## rebuild en locale strings and push to master (req: GH_TOKEN)
 	@git push -u origin-tx master
 
 test/%: ## run tests against a stack (only common tests or common tests + specific tests)
-	@if [ ! -d "$(notdir $@)/test" ]; then TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest test; else TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest test $(notdir $@)/test; fi
+	@if [ ! -d "$(notdir $@)/test" ]; then TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test; \
+	else TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test $(notdir $@)/test; fi

docs/contributing/packages.md

@@ -13,3 +13,20 @@ make build/somestack-notebook
 4. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request) (PR) with your changes.
 5. Watch for Travis to report a build success or failure for your PR on GitHub.
 6. Discuss changes with the maintainers and address any build issues. Version conflicts are the most common problem. You may need to upgrade additional packages to fix build failures.
+
+## Notes
+
+In order to help identifying packages that can be updated you can use the following helper tool.
+It will list all the packages installed in the `Dockerfile` that can be updated -- dependencies are filtered to focus only on requested packages.
+
+```bash
+$ make check-outdated/base-notebook
+
+# INFO     test_outdated:test_outdated.py:80 3/8 (38%) packages could be updated
+# INFO     test_outdated:test_outdated.py:82 
+# Package     Current    Newest
+# ----------  ---------  --------
+# conda       4.7.12     4.8.2
+# jupyterlab  1.2.5      2.0.0
+# python      3.7.4      3.8.2
+```

docs/using/recipes.md

@@ -22,7 +22,7 @@ docker run -it -e GRANT_SUDO=yes --user root jupyter/minimal-notebook
 ```
 
 **You should only enable `sudo` if you trust the user and/or if the container is running on an
-isolated host.**
+isolated host.** See [Docker security documentation](https://docs.docker.com/engine/security/userns-remap/) for more information about running containers as `root`.
 
 ## Using `pip install` or `conda install` in a Child Docker image
 

pytest.ini

 [pytest]
-addopts = -rA
+addopts = -ra
 log_cli = 1
 log_cli_level = INFO
 log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)
-log_cli_date_format=%Y-%m-%d %H:%M:%S
\ No newline at end of file
+log_cli_date_format=%Y-%m-%d %H:%M:%S
+markers =
+    info: marks tests as info (deselect with '-m "not info"')
\ No newline at end of file

requirements-dev.txt

@@ -4,4 +4,6 @@ recommonmark==0.5.0
 requests
 sphinx>=1.6
 sphinx-intl
+tabulate
 transifex-client
+

scipy-notebook/Dockerfile

@@ -26,6 +26,7 @@ RUN conda install --quiet --yes \
     'h5py=2.10.*' \
     'hdf5=1.10.*' \
     'ipywidgets=7.5.*' \
+    'ipympl=0.5.*'\
     'matplotlib-base=3.1.*' \
     'numba=0.48.*' \
     'numexpr=2.7.*' \
@@ -40,6 +41,7 @@ RUN conda install --quiet --yes \
     'statsmodels=0.11.*' \
     'sympy=1.5.*' \
     'vincent=0.4.*' \
+    'widgetsnbextension=3.5.*'\
     'xlrd' \
     && \
     conda clean --all -f -y && \
@@ -48,8 +50,9 @@ RUN conda install --quiet --yes \
     # Also activate ipywidgets extension for JupyterLab
     # Check this URL for most recent compatibilities
     # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
-    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.1.0 --no-build && \
     jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \
+    jupyter labextension install jupyter-matplotlib --no-build && \
     jupyter lab build && \
     npm cache clean --force && \
     rm -rf $CONDA_DIR/share/jupyter/lab/staging && \

test/helpers.py

+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+# CondaPackageHelper is partially based on the work https://oerpli.github.io/post/2019/06/conda-outdated/.
+# See copyright below.
+#
+# MIT License
+# Copyright (c) 2019 Abraham Hinteregger
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import re
+from collections import defaultdict
+from itertools import chain
+import logging
+import json
+
+from tabulate import tabulate
+
+LOGGER = logging.getLogger(__name__)
+
+
+class CondaPackageHelper:
+    """Conda package helper permitting to get information about packages
+    """
+
+    def __init__(self, container):
+        # if isinstance(container, TrackedContainer):
+        self.running_container = CondaPackageHelper.start_container(container)
+        self.specs = None
+        self.installed = None
+        self.available = None
+        self.comparison = None
+
+    @staticmethod
+    def start_container(container):
+        """Start the TrackedContainer and return an instance of a running container"""
+        LOGGER.info(f"Starting container {container.image_name} ...")
+        return container.run(
+            tty=True, command=["start.sh", "bash", "-c", "sleep infinity"]
+        )
+
+    @staticmethod
+    def _conda_export_command(from_history=False):
+        """Return the conda export command with or without history"""
+        cmd = ["conda", "env", "export", "-n", "base", "--json", "--no-builds"]
+        if from_history:
+            cmd.append("--from-history")
+        return cmd
+
+    def installed_packages(self):
+        """Return the installed packages"""
+        if self.installed is None:
+            LOGGER.info(f"Grabing the list of installed packages ...")
+            self.installed = CondaPackageHelper._packages_from_json(
+                self._execute_command(CondaPackageHelper._conda_export_command())
+            )
+        return self.installed
+
+    def specified_packages(self):
+        """Return the specifications (i.e. packages installation requested)"""
+        if self.specs is None:
+            LOGGER.info(f"Grabing the list of specifications ...")
+            self.specs = CondaPackageHelper._packages_from_json(
+                self._execute_command(CondaPackageHelper._conda_export_command(True))
+            )
+        return self.specs
+
+    def _execute_command(self, command):
+        """Execute a command on a running container"""
+        rc = self.running_container.exec_run(command)
+        return rc.output.decode("utf-8")
+
+    @staticmethod
+    def _packages_from_json(env_export):
+        """Extract packages and versions from the lines returned by the list of specifications"""
+        dependencies = json.loads(env_export).get("dependencies")
+        packages_list = map(lambda x: x.split("=", 1), dependencies)
+        # TODO: could be improved
+        return {package[0]: set(package[1:]) for package in packages_list}
+
+    def available_packages(self):
+        """Return the available packages"""
+        if self.available is None:
+            LOGGER.info(
+                f"Grabing the list of available packages (can take a while) ..."
+            )
+            # Keeping command line output since `conda search --outdated --json` is way too long ...
+            self.available = CondaPackageHelper._extract_available(
+                self._execute_command(["conda", "search", "--outdated"])
+            )
+        return self.available
+
+    @staticmethod
+    def _extract_available(lines):
+        """Extract packages and versions from the lines returned by the list of packages"""
+        ddict = defaultdict(set)
+        for line in lines.splitlines()[2:]:
+            pkg, version = re.match(r"^(\S+)\s+(\S+)", line, re.MULTILINE).groups()
+            ddict[pkg].add(version)
+        return ddict
+
+    def check_updatable_packages(self, specifications_only=True):
+        """Check the updatables packages including or not dependencies"""
+        specs = self.specified_packages()
+        installed = self.installed_packages()
+        available = self.available_packages()
+        self.comparison = list()
+        for pkg, inst_vs in self.installed.items():
+            if not specifications_only or pkg in specs:
+                avail_vs = sorted(
+                    list(available[pkg]), key=CondaPackageHelper.semantic_cmp
+                )
+                if not avail_vs:
+                    continue
+                current = min(inst_vs, key=CondaPackageHelper.semantic_cmp)
+                newest = avail_vs[-1]
+                if avail_vs and current != newest:
+                    if CondaPackageHelper.semantic_cmp(
+                        current
+                    ) < CondaPackageHelper.semantic_cmp(newest):
+                        self.comparison.append(
+                            {"Package": pkg, "Current": current, "Newest": newest}
+                        )
+        return self.comparison
+
+    @staticmethod
+    def semantic_cmp(version_string):
+        """Manage semantic versioning for comparison"""
+
+        def mysplit(string):
+            version_substrs = lambda x: re.findall(r"([A-z]+|\d+)", x)
+            return list(chain(map(version_substrs, string.split("."))))
+
+        def str_ord(string):
+            num = 0
+            for char in string:
+                num *= 255
+                num += ord(char)
+            return num
+
+        def try_int(version_str):
+            try:
+                return int(version_str)
+            except ValueError:
+                return str_ord(version_str)
+
+        mss = list(chain(*mysplit(version_string)))
+        return tuple(map(try_int, mss))
+
+    def get_outdated_summary(self, specifications_only=True):
+        """Return a summary of outdated packages"""
+        if specifications_only:
+            nb_packages = len(self.specs)
+        else:
+            nb_packages = len(self.installed)
+        nb_updatable = len(self.comparison)
+        updatable_ratio = nb_updatable / nb_packages
+        return f"{nb_updatable}/{nb_packages} ({updatable_ratio:.0%}) packages could be updated"
+
+    def get_outdated_table(self):
+        """Return a table of outdated packages"""
+        return tabulate(self.comparison, headers="keys")

test/test_outdated.py

+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+import logging
+
+import pytest
+
+from helpers import CondaPackageHelper
+
+LOGGER = logging.getLogger(__name__)
+
+
+@pytest.mark.info
+def test_outdated_packages(container, specifications_only=True):
+    """Getting the list of updatable packages"""
+    LOGGER.info(f"Checking outdated packages in {container.image_name} ...")
+    pkg_helper = CondaPackageHelper(container)
+    pkg_helper.check_updatable_packages(specifications_only)
+    LOGGER.info(pkg_helper.get_outdated_summary(specifications_only))
+    LOGGER.info(f"\n{pkg_helper.get_outdated_table()}\n")