From 8c081cab1cd923651ccf0858c3dece168e559966 Mon Sep 17 00:00:00 2001 From: John Harwell Date: Tue, 18 Oct 2022 15:02:59 -0500 Subject: [PATCH 1/3] enh(#311): Usability improvements - Better debug logging config - Helpful message when it crashes --- README.rst | 7 ------- docs/conf.py | 2 +- setup.py | 3 ++- sierra/core/logging.py | 21 ++++++--------------- sierra/main.py | 21 +++++++++++++++++++++ sierra/version.py | 2 +- todo.org | 10 ++++++++-- 7 files changed, 39 insertions(+), 27 deletions(-) diff --git a/README.rst b/README.rst index 8114c15b..8196d908 100755 --- a/README.rst +++ b/README.rst @@ -14,13 +14,6 @@ SIERRA (reSearch pIpEline for Reproducibility, Reusability, and Automation) .. |linux-supported| image:: https://svgshare.com/i/Zhy.svg .. |osx-supported| image:: https://svgshare.com/i/ZjP.svg -.. - .. image:: https://img.shields.io/badge/python-3.8-blue.svg - :target: https://www.python.org/downloads/release/python-380/ - - .. image:: https://img.shields.io/badge/python-3.9-blue.svg - :target: https://www.python.org/downloads/release/python-390/ - .. |ci-integration-master| image:: https://github.com/jharwell/sierra/actions/workflows/integration-all.yml/badge.svg?branch=master .. |ci-analysis-master| image:: https://github.com/jharwell/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=master .. |ci-coverage-master| image:: https://coveralls.io/repos/github/jharwell/sierra/badge.svg?branch=master diff --git a/docs/conf.py b/docs/conf.py index f3ffa7e3..23fc611c 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -51,7 +51,7 @@ 'xref', 'sphinx_last_updated_by_git', 'sphinx_rtd_theme', - 'sphinxcontrib.napoleon', + 'sphinx.ext.napoleon', 'autoapi.sphinx', 'sphinx.ext.autosummary'] diff --git a/setup.py b/setup.py index 65578565..fd798a52 100644 --- a/setup.py +++ b/setup.py @@ -88,6 +88,7 @@ "psutil", "distro", "netifaces", + "haggis", "coloredlogs", "implements", @@ -98,7 +99,7 @@ extras_require={ "devel": [ # checkers, CI, etc. - 'pylint', + 'pylint==2.14.5', # Temporarily, until the default 2.15.0 is fixed/superseded 'pytype', 'pydocstyle', 'xenon', diff --git a/sierra/core/logging.py b/sierra/core/logging.py index 5322ae01..b5e27501 100755 --- a/sierra/core/logging.py +++ b/sierra/core/logging.py @@ -28,25 +28,16 @@ # 3rd party packages import coloredlogs +from haggis import logs # Project packages -TRACE = logging.DEBUG - 5 - - -def initialize(log_level): - def log_for_level(self, message, *args, **kwargs): - if self.isEnabledFor(TRACE): - self._log(TRACE, message, args, **kwargs) - - def log_to_root(message, *args, **kwargs): - logging.log(TRACE, message, *args, **kwargs) - - logging.addLevelName(TRACE, "TRACE") - setattr(logging, "TRACE", TRACE) - setattr(logging.getLoggerClass(), "trace", log_for_level) - setattr(logging, "trace", log_to_root) +def initialize(log_level: str): + logs.add_logging_level(level_name='TRACE', + level_num=logging.DEBUG - 5, + method_name=None, + if_exists=logs.RAISE) # Needed for static analysis (mypy and/or pylint) setattr(logging, '_HAS_DYNAMIC_ATTRIBUTES', True) diff --git a/sierra/main.py b/sierra/main.py index 4cffc42b..732484e2 100755 --- a/sierra/main.py +++ b/sierra/main.py @@ -37,6 +37,8 @@ import sierra.core.startup import sierra.version +kIssuesURL = "https://github.com/jharwell/sierra/issues" + class SIERRA(): """Initialize SIERRA and then launch the pipeline.""" @@ -138,12 +140,31 @@ def __call__(self) -> None: sys.exit() +def excepthook(exc_type, exc_value, exc_traceback): + logging.fatal(("SIERRA has encountered an unexpected error and will now " + "terminate.\n\n" + "If you think this is a bug, please report it at:\n\n%s\n\n" + "When reporting, please include as much information as you " + "can. Ideally:\n\n" + "1. The below traceback.\n" + "2. The exact command you used to run sierra-cli.\n" + "3. sierra-cli's logging output in the terminal.\n\n" + "In some cases, creating a Minimum Working Example (MWE) " + "reproducing the error with specific input files and/or " + "data is also helpful for quick triage and fix.\n"), + kIssuesURL, + exc_info=(exc_type, exc_value, exc_traceback)) + + def main(): # Necessary on OSX, because python > 3.8 defaults to "spawn" which does not # copy loaded modules, which results in the singleton plugin managers not # working. mp.set_start_method("fork") + # Nice traceback on unexpected errors + sys.excepthook = excepthook + # Bootstrap the cmdline to print version if needed bootstrap = cmd.BootstrapCmdline() bootstrap_args, _ = bootstrap.parser.parse_known_args() diff --git a/sierra/version.py b/sierra/version.py index 7795d36a..b4c53636 100644 --- a/sierra/version.py +++ b/sierra/version.py @@ -20,4 +20,4 @@ # Project packages -__version__ = "1.2.22" +__version__ = "1.2.23" diff --git a/todo.org b/todo.org index d7820faa..fc953125 100644 --- a/todo.org +++ b/todo.org @@ -27,8 +27,8 @@ files. This will allow me to easily parameterize multiple versions of python, AND reduce the # of jobs I need/total workflow runtime on github by a good bit. -** TODO Switch from cmdopts dictionary to a data class with fields--I will get -WAY better help from the static analyzer +** TODO Switch from cmdopts dictionary to a data class with fields +I will get WAY better help from the static analyzer ** TODO Add quick quick start: a linux VM with SIERRA all set up and ready to go @@ -161,3 +161,9 @@ This really should be there.... And not require a valid --project to be passed. cohesion ** DONE Make bivariate inter-experiment heatmaps renderable into videos CLOSED: [2022-08-25 Thu 12:56] +** DONE Switch from my logging hack to haggis module +CLOSED: [2022-10-18 Tue 15:02] +Does what I do, but much better + +** DONE Add sys.excepthook hook asking the user to file a bug. +CLOSED: [2022-10-18 Tue 15:02] From d563bc4862bc1ab1c2f2813dad58392973601681 Mon Sep 17 00:00:00 2001 From: John Harwell Date: Sun, 20 Nov 2022 14:48:15 -0600 Subject: [PATCH 2/3] bugfix(#312): pathlib symlinks - Also fix startup so that stuff is checkd again for linux mint; newer versions of the apt python package change syntax slightly. --- README.rst | 2 +- sierra/core/pipeline/stage5/intra_scenario_comparator.py | 1 - sierra/core/root_dirpath_generator.py | 6 +++++- sierra/core/startup.py | 8 ++++---- sierra/main.py | 8 +++++--- sierra/version.py | 2 +- 6 files changed, 16 insertions(+), 11 deletions(-) diff --git a/README.rst b/README.rst index 8196d908..da9714a3 100755 --- a/README.rst +++ b/README.rst @@ -29,7 +29,7 @@ SIERRA (reSearch pIpEline for Reproducibility, Reusability, and Automation) :target: https://zenodo.org/badge/latestdoi/125774567 .. |docs| image:: https://readthedocs.org/projects/sierra/badge/?version=master - :target: https://readthedocs.org/projects/sierra/master + :target: https://sierra.readthedocs.io/en/master/ .. |maintenance| image:: https://img.shields.io/badge/Maintained%3F-yes-green.svg :target: https://gitHub.com/jharwell/sierra/graphs/commit-activity diff --git a/sierra/core/pipeline/stage5/intra_scenario_comparator.py b/sierra/core/pipeline/stage5/intra_scenario_comparator.py index 4a9d6a8c..0393d6d6 100755 --- a/sierra/core/pipeline/stage5/intra_scenario_comparator.py +++ b/sierra/core/pipeline/stage5/intra_scenario_comparator.py @@ -689,7 +689,6 @@ def _gen_paired_heatmaps(self, for i in range(1, len(paths)): df = reader(paths[i]) - print(paths[i]) if comp_type == 'HMscale': plot_df = df / ref_df elif comp_type == 'HMdiff': diff --git a/sierra/core/root_dirpath_generator.py b/sierra/core/root_dirpath_generator.py index 23ae8ca6..b9ccb363 100755 --- a/sierra/core/root_dirpath_generator.py +++ b/sierra/core/root_dirpath_generator.py @@ -197,7 +197,11 @@ def gen_batch_root(root: str, """ batch_leaf = gen_batch_leaf(criteria, template_stem, scenario) - sierra_root = pathlib.Path(root).resolve() + + # Don't reslove() the path--that makes symlinked dirs under $HOME through + # errors which are fatal from pathlib's POV, but actually harmless. + sierra_root = pathlib.Path(root) + return sierra_root / project / controller / batch_leaf diff --git a/sierra/core/startup.py b/sierra/core/startup.py index 7d80e1ca..8eaa61d0 100644 --- a/sierra/core/startup.py +++ b/sierra/core/startup.py @@ -85,8 +85,8 @@ def _linux_pkg_checks() -> None: dist = distro.id() os_info = distro.os_release_info() - - if os_info['id_like'] in ['debian', 'ubuntu']: + if any(candidate in os_info['id_like'] for candidate in ['debian', + 'ubuntu']): _apt_pkg_checks(dist) else: logging.warning(("Unknown Linux distro '%s' detected: skipping package " @@ -125,8 +125,8 @@ def _apt_pkg_checks(dist: str) -> None: logging.debug(("Recommended .deb packages %s missing on Linux " "distribution '%s'. Some SIERRA functionality will " "not be available. "), - dist, - missing) + missing, + dist) def _osx_pkg_checks() -> None: diff --git a/sierra/main.py b/sierra/main.py index 732484e2..11851d95 100755 --- a/sierra/main.py +++ b/sierra/main.py @@ -146,9 +146,11 @@ def excepthook(exc_type, exc_value, exc_traceback): "If you think this is a bug, please report it at:\n\n%s\n\n" "When reporting, please include as much information as you " "can. Ideally:\n\n" - "1. The below traceback.\n" - "2. The exact command you used to run sierra-cli.\n" - "3. sierra-cli's logging output in the terminal.\n\n" + "1. What you were trying to do in SIERRA.\n" + "2. The terminal output of sierra-cli, including the " + "below traceback.\n" + "3. The exact command you used to run SIERRA.\n" + "\n" "In some cases, creating a Minimum Working Example (MWE) " "reproducing the error with specific input files and/or " "data is also helpful for quick triage and fix.\n"), diff --git a/sierra/version.py b/sierra/version.py index b4c53636..8ded3c6c 100644 --- a/sierra/version.py +++ b/sierra/version.py @@ -20,4 +20,4 @@ # Project packages -__version__ = "1.2.23" +__version__ = "1.2.24" From 4827a31b145538edc428e24c986c08b4893b88e1 Mon Sep 17 00:00:00 2001 From: John Harwell Date: Mon, 16 Jan 2023 11:31:26 -0600 Subject: [PATCH 3/3] Switch to MIT license --- .../actions/sample-project-setup/action.yml | 19 +- .github/actions/sierra-setup/action.yml | 42 +- .github/workflows/coverage.yml | 33 +- .github/workflows/exec-env-plugins.yml | 6 +- .github/workflows/integration-all.yml | 10 +- .github/workflows/ros1gazebo.yml | 12 +- .github/workflows/static-analysis.yml | 9 +- .github/workflows/unit-tests.yml | 1 - LICENSE | 18 + LICENSE.md | 674 ------------------ README.rst | 3 +- noxfile.py | 2 +- setup.py | 4 +- sierra/__init__.py | 14 +- sierra/core/__init__.py | 14 +- sierra/core/cmdline.py | 16 +- sierra/core/config.py | 17 +- sierra/core/experiment/__init__.py | 14 +- sierra/core/experiment/bindings.py | 14 +- sierra/core/experiment/definition.py | 14 +- sierra/core/experiment/spec.py | 14 +- sierra/core/experiment/xml.py | 14 +- .../generators/controller_generator_parser.py | 14 +- sierra/core/generators/exp_creator.py | 14 +- sierra/core/generators/exp_generators.py | 14 +- sierra/core/generators/generator_factory.py | 14 +- sierra/core/graphs/heatmap.py | 14 +- sierra/core/graphs/scatterplot2D.py | 14 +- sierra/core/graphs/stacked_line_graph.py | 14 +- sierra/core/graphs/stacked_surface_graph.py | 14 +- sierra/core/graphs/summary_line_graph.py | 14 +- sierra/core/hpc/__init__.py | 14 +- sierra/core/hpc/cmdline.py | 14 +- sierra/core/logging.py | 14 +- sierra/core/models/__init__.py | 14 +- sierra/core/models/graphs.py | 14 +- sierra/core/models/interface.py | 14 +- sierra/core/pipeline/__init__.py | 14 +- sierra/core/pipeline/pipeline.py | 14 +- sierra/core/pipeline/stage1/__init__.py | 1 - .../core/pipeline/stage1/pipeline_stage1.py | 14 +- sierra/core/pipeline/stage2/__init__.py | 1 - sierra/core/pipeline/stage2/exp_runner.py | 14 +- .../core/pipeline/stage2/pipeline_stage2.py | 14 +- sierra/core/pipeline/stage3/__init__.py | 1 - sierra/core/pipeline/stage3/imagizer.py | 14 +- .../core/pipeline/stage3/pipeline_stage3.py | 14 +- sierra/core/pipeline/stage3/run_collator.py | 14 +- .../pipeline/stage3/statistics_calculator.py | 14 +- sierra/core/pipeline/stage4/__init__.py | 3 - sierra/core/pipeline/stage4/graph_collator.py | 14 +- .../stage4/inter_exp_graph_generator.py | 14 +- .../stage4/intra_exp_graph_generator.py | 14 +- sierra/core/pipeline/stage4/model_runner.py | 14 +- .../core/pipeline/stage4/pipeline_stage4.py | 14 +- sierra/core/pipeline/stage4/rendering.py | 14 +- .../pipeline/stage4/yaml_config_loader.py | 14 +- sierra/core/pipeline/stage5/__init__.py | 1 - .../stage5/inter_scenario_comparator.py | 14 +- .../stage5/intra_scenario_comparator.py | 14 +- .../core/pipeline/stage5/pipeline_stage5.py | 14 +- sierra/core/platform.py | 14 +- sierra/core/plugin.py | 14 +- sierra/core/plugin_manager.py | 14 +- sierra/core/root_dirpath_generator.py | 14 +- sierra/core/ros1/__init__.py | 14 +- sierra/core/ros1/callbacks.py | 14 +- sierra/core/ros1/cmdline.py | 14 +- sierra/core/ros1/generators.py | 14 +- sierra/core/ros1/variables/__init__.py | 14 +- sierra/core/ros1/variables/exp_setup.py | 14 +- sierra/core/startup.py | 14 +- sierra/core/stat_kernels.py | 14 +- sierra/core/storage.py | 14 +- sierra/core/types.py | 14 +- sierra/core/utils.py | 14 +- sierra/core/variables/__init__.py | 14 +- sierra/core/variables/base_variable.py | 14 +- sierra/core/variables/batch_criteria.py | 14 +- sierra/core/variables/exp_setup.py | 14 +- sierra/core/variables/population_size.py | 14 +- sierra/core/variables/variable_density.py | 14 +- sierra/core/vector.py | 14 +- sierra/main.py | 14 +- sierra/plugins/__init__.py | 14 +- sierra/plugins/hpc/__init__.py | 14 +- sierra/plugins/hpc/adhoc/__init__.py | 14 +- sierra/plugins/hpc/adhoc/plugin.py | 14 +- sierra/plugins/hpc/local/__init__.py | 14 +- sierra/plugins/hpc/local/plugin.py | 14 +- sierra/plugins/hpc/pbs/__init__.py | 14 +- sierra/plugins/hpc/pbs/plugin.py | 14 +- sierra/plugins/hpc/slurm/__init__.py | 14 +- sierra/plugins/hpc/slurm/plugin.py | 14 +- sierra/plugins/platform/__init__.py | 14 +- sierra/plugins/platform/argos/__init__.py | 14 +- sierra/plugins/platform/argos/cmdline.py | 14 +- .../platform/argos/generators/__init__.py | 14 +- .../argos/generators/platform_generators.py | 14 +- sierra/plugins/platform/argos/plugin.py | 22 +- .../platform/argos/variables/__init__.py | 14 +- .../platform/argos/variables/arena_shape.py | 14 +- .../platform/argos/variables/cameras.py | 14 +- .../argos/variables/constant_density.py | 14 +- .../platform/argos/variables/exp_setup.py | 14 +- .../argos/variables/physics_engines.py | 14 +- .../variables/population_constant_density.py | 14 +- .../argos/variables/population_size.py | 14 +- .../variables/population_variable_density.py | 14 +- .../platform/argos/variables/rendering.py | 14 +- .../plugins/platform/ros1gazebo/__init__.py | 14 +- sierra/plugins/platform/ros1gazebo/cmdline.py | 14 +- .../ros1gazebo/generators/__init__.py | 14 +- .../generators/platform_generators.py | 14 +- sierra/plugins/platform/ros1gazebo/plugin.py | 14 +- .../platform/ros1gazebo/variables/__init__.py | 14 +- .../ros1gazebo/variables/population_size.py | 14 +- sierra/plugins/platform/ros1robot/__init__.py | 14 +- sierra/plugins/platform/ros1robot/cmdline.py | 14 +- .../platform/ros1robot/generators/__init__.py | 14 +- .../generators/platform_generators.py | 14 +- sierra/plugins/platform/ros1robot/plugin.py | 14 +- .../platform/ros1robot/variables/__init__.py | 14 +- .../ros1robot/variables/population_size.py | 14 +- sierra/plugins/robot/__init__.py | 14 +- sierra/plugins/robot/turtlebot3/__init__.py | 14 +- sierra/plugins/robot/turtlebot3/plugin.py | 14 +- sierra/plugins/storage/__init__.py | 14 +- sierra/plugins/storage/csv/__init__.py | 14 +- sierra/plugins/storage/csv/plugin.py | 14 +- sierra/version.py | 17 +- 131 files changed, 221 insertions(+), 2217 deletions(-) create mode 100644 LICENSE delete mode 100755 LICENSE.md diff --git a/.github/actions/sample-project-setup/action.yml b/.github/actions/sample-project-setup/action.yml index 7da547a7..02dbaeef 100644 --- a/.github/actions/sample-project-setup/action.yml +++ b/.github/actions/sample-project-setup/action.yml @@ -37,10 +37,12 @@ runs: shell: bash working-directory: ../../ run: | + # 2023/01/16: || true needed because homebrew installation of whatever + # dependencies these packages requires manual intervention to fix, and I + # don't have a mac. if [ "${{ runner.os }}" == "macOS" ]; then - brew update brew install pkg-config cmake libpng freeimage lua qt \ - docbook asciidoc graphviz doxygen + docbook asciidoc graphviz doxygen|| true elif [ "${{ runner.os }}" == "Linux" ]; then sudo apt-get update sudo apt-get install cmake libfreeimage-dev libfreeimageplus-dev \ @@ -89,6 +91,19 @@ runs: sudo apt-get install ros-${{ inputs.rosdistro }}-turtlebot3-msgs sudo apt-get install ros-${{ inputs.rosdistro }}-turtlebot3-gazebo sudo apt-get install ros-${{ inputs.rosdistro }}-turtlebot3-bringup + sudo apt-get install python${{ matrix.python-version }} python${{ matrix.python-version }}-dev + sudo apt-get install python${{ matrix.python-version }}-venv python3-apt + sudo apt-get install python3-pip python3-cairo intltool python3-wheel python3-rospkg python3-empy + + # 2023/1/18: You still need install these even after installing stuff + # with apt AND if the sysem python matches your current python. I don't + # know why. + pip3 install empy + pip3 install rospkg wheel pyparsing pyqt5 + pip3 install pyqt5 pysip numpy rospkg + pip3 install matplotlib pyyaml psutil + pip3 install pysip defusedxml pyparsing pydev + pip3 install pyopengl opencv-python - name: Install SIERRA ROSBridge dependency (ubuntu) if: inputs.platform == 'ros1gazebo' diff --git a/.github/actions/sierra-setup/action.yml b/.github/actions/sierra-setup/action.yml index c958e2f2..462989ca 100644 --- a/.github/actions/sierra-setup/action.yml +++ b/.github/actions/sierra-setup/action.yml @@ -16,23 +16,29 @@ runs: # Ubuntu setup ############################################################################ - name: Setup python (ubuntu) + uses: actions/setup-python@v4 if: runner.os == 'Linux' - shell: bash - run: | - # apt fails randomly on microsoft's azure servers... - sudo sed -i 's/azure\.//' /etc/apt/sources.list - sudo add-apt-repository -y ppa:deadsnakes/ppa + with: + python-version: ${{ matrix.python-version }} - sudo apt-get update + # - uses: Setup python (ubuntu) + # if: runner.os == 'Linux' + # shell: bash + # run: | + # # apt fails randomly on microsoft's azure servers... + # sudo sed -i 's/azure\.//' /etc/apt/sources.list + # sudo add-apt-repository -y ppa:deadsnakes/ppa + + # sudo apt-get update - sudo apt-get install python${{ matrix.python-version }} python${{ matrix.python-version }}-dev - sudo apt-get install python${{ matrix.python-version }}-venv python3-apt - sudo apt-get install python3-pip python3-cairo intltool python3-wheel strace - sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${{ matrix.python-version }} 1 + # sudo apt-get install python${{ matrix.python-version }} python${{ matrix.python-version }}-dev + # sudo apt-get install python${{ matrix.python-version }}-venv python3-apt + # sudo apt-get install python3-pip python3-cairo intltool python3-wheel strace + # sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${{ matrix.python-version }} 1 - # HACK HACK HACK! - sudo ln -s /usr/lib/python3/dist-packages/apt_pkg.cpython-38-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/apt_pkg.so - sudo ln -s /usr/lib/python3/dist-packages/netifaces.cpython-38-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/netifaces.so + # # HACK HACK HACK! + # sudo ln -s /usr/lib/python3/dist-packages/apt_pkg.cpython-38-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/apt_pkg.so + # sudo ln -s /usr/lib/python3/dist-packages/netifaces.cpython-38-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/netifaces.so - name: Install system deps (ubuntu) @@ -59,10 +65,12 @@ runs: shell: bash if: runner.os == 'macOS' run: | - brew update - brew install parallel pssh ffmpeg - brew install --cask mactex - brew install --cask xquartz + # 2023/01/16: || true needed because homebrew installation of whatever + # dependencies these packages requires manual intervention to fix, and I + # don't have a mac. + brew install parallel pssh ffmpeg || true + brew install --cask mactex || true + brew install --cask xquartz || true python -m pip install --upgrade pip python -m pip install wheel diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 0fb690b3..f0c8059e 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -1,9 +1,16 @@ name: Coverage CI +# Run: +# +# - Every month. Scheduling helps keep drift/issues with updates +# to runners at bay. +# - On pushes. on: push: paths: - 'sierra/**' + schedule: + - cron: '0 0 1 * *' jobs: argos-ci: @@ -42,38 +49,14 @@ jobs: with: os: ubuntu-20.04 - # docs: - # runs-on: ubuntu-latest - # strategy: - # matrix: - # python-version: - # - 3.9 - # steps: - # - uses: actions/checkout@v3 - # - uses: ./.github/actions/sierra-setup - - # - name: Build docs - # shell: bash - # run: | - # cd docs && coverage run $(which sphinx-build) -M html "." "_build" - # cd docs && coverage combine - # cd docs && coverage report - # cd docs && coverage xml - - # - uses: actions/upload-artifact@v3 - # with: - # name: ci-sphinx-docs-${{ runner.os }}-${{ matrix.python-version }}-coverage - # path: docs/.coverage.* - coverage: runs-on: ubuntu-latest strategy: matrix: python-version: - - 3.9 + - 3.8 needs: - # - docs - unit-tests - argos-ci - ros1gazebo-ci diff --git a/.github/workflows/exec-env-plugins.yml b/.github/workflows/exec-env-plugins.yml index a42dfe6b..cc26ebd0 100644 --- a/.github/workflows/exec-env-plugins.yml +++ b/.github/workflows/exec-env-plugins.yml @@ -20,9 +20,10 @@ jobs: runs-on: ${{ inputs.os }} strategy: matrix: + # You CANNOT use python 3.9 with ubuntu 20.04 with ROS, because 3.8 is + # the system python and things just don't work otherwise... python-version: - 3.8 - - 3.9 steps: - uses: actions/checkout@v3 @@ -50,9 +51,10 @@ jobs: runs-on: ${{ inputs.os }} strategy: matrix: + # You CANNOT use python 3.9 with ubuntu 20.04 with ROS, because 3.8 is + # the system python and things just don't work otherwise... python-version: - 3.8 - - 3.9 steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/integration-all.yml b/.github/workflows/integration-all.yml index 748dd7c3..1eff0f23 100644 --- a/.github/workflows/integration-all.yml +++ b/.github/workflows/integration-all.yml @@ -1,10 +1,18 @@ name: Integration Tests +# Run: +# +# - Every month. Scheduling helps keep drift/issues with updates +# to runners at bay. +# - On pushes. on: push: paths: - 'sierra/**' + schedule: + - cron: '0 0 1 * *' + jobs: argos-ci-ubuntu: uses: ./.github/workflows/argos.yml @@ -53,7 +61,7 @@ jobs: strategy: matrix: python-version: - - 3.9 + - 3.8 needs: - argos-ci-ubuntu - argos-ci-osx diff --git a/.github/workflows/ros1gazebo.yml b/.github/workflows/ros1gazebo.yml index f10855a7..57b27d3a 100644 --- a/.github/workflows/ros1gazebo.yml +++ b/.github/workflows/ros1gazebo.yml @@ -7,21 +7,16 @@ on: os: required: True type: string - # push: - # branches: - # # - master - # # - devel - # paths: - # - 'sierra/**' jobs: bc-univar-sanity: runs-on: ${{ inputs.os }} strategy: matrix: + # You CANNOT use python 3.9 with ubuntu 20.04 with ROS, because 3.8 is + # the system python and things just don't work otherwise... python-version: - 3.8 - - 3.9 steps: - uses: actions/checkout@v3 @@ -47,9 +42,10 @@ jobs: runs-on: ${{ inputs.os }} strategy: matrix: + # You CANNOT use python 3.9 with ubuntu 20.04 with ROS, because 3.8 is + # the system python and things just don't work otherwise... python-version: - 3.8 - - 3.9 steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml index 13503989..8ca279b9 100644 --- a/.github/workflows/static-analysis.yml +++ b/.github/workflows/static-analysis.yml @@ -1,10 +1,17 @@ name: Static Analysis +# Run: +# +# - Every month. Scheduling helps keep drift/issues with updates +# to runners at bay. +# - On pushes. on: - workflow_call: push: paths: - 'sierra/**' + schedule: + - cron: '0 0 1 * *' + jobs: analyze: diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index b8585a38..f9537b80 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -28,7 +28,6 @@ jobs: which sierra-cli which python3 nox --pythons ${{ matrix.python-version }} --sessions unit_tests - ls -alh - uses: actions/upload-artifact@v3 with: diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..62b09bca --- /dev/null +++ b/LICENSE @@ -0,0 +1,18 @@ +Copyright 2022 John Harwell + +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. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/README.rst b/README.rst index da9714a3..508780ea 100755 --- a/README.rst +++ b/README.rst @@ -22,8 +22,7 @@ SIERRA (reSearch pIpEline for Reproducibility, Reusability, and Automation) .. |ci-analysis-devel| image:: https://github.com/jharwell/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=devel .. |ci-coverage-devel| image:: https://coveralls.io/repos/github/jharwell/sierra/badge.svg?branch=devel -.. |license| image:: https://img.shields.io/badge/License-GPLv3-blue.svg - :target: https://www.gnu.org/licenses/gpl-3.0 +.. |license| image:: https://img.shields.io/badge/License-MIT-blue.svg .. |doi| image:: https://zenodo.org/badge/125774567.svg :target: https://zenodo.org/badge/latestdoi/125774567 diff --git a/noxfile.py b/noxfile.py index 6879e408..03ce9735 100644 --- a/noxfile.py +++ b/noxfile.py @@ -47,7 +47,7 @@ def lint(session): session.run('xenon', '--max-absolute C', '--max-modules B', - '--max-average A' + '--max-average A', '--no-assert sierra') diff --git a/setup.py b/setup.py index fd798a52..f8c351b6 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ url="https://github.com/jharwell/sierra", author="John Harwell", author_email="john.r.harwell@gmail.com", - license="GPLv3+", + license="MIT", platforms=['linux', 'osx'], keywords=['research', 'automation', @@ -56,7 +56,7 @@ # "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", - "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", + "License :: OSI Approved :: MIT License", "Environment :: Console", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX :: Linux", diff --git a/sierra/__init__.py b/sierra/__init__.py index 20402b82..a80e0b05 100755 --- a/sierra/__init__.py +++ b/sierra/__init__.py @@ -1,18 +1,6 @@ # Copyright 2021 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see \n" + "License: MIT.\n" "This is free software: you are free to change and redistribute it.\n" "SIERRA comes with no warranty.\n\n" diff --git a/sierra/core/config.py b/sierra/core/config.py index bec21c0a..9f760c0a 100755 --- a/sierra/core/config.py +++ b/sierra/core/config.py @@ -1,18 +1,6 @@ # Copyright 2020 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see `. diff --git a/sierra/core/pipeline/stage4/pipeline_stage4.py b/sierra/core/pipeline/stage4/pipeline_stage4.py index b6c0d4d9..ded2fdaf 100755 --- a/sierra/core/pipeline/stage4/pipeline_stage4.py +++ b/sierra/core/pipeline/stage4/pipeline_stage4.py @@ -1,18 +1,6 @@ # Copyright 2018 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see ` using :term:`ROS1`. diff --git a/sierra/core/ros1/cmdline.py b/sierra/core/ros1/cmdline.py index a1d074d1..bc96dc39 100644 --- a/sierra/core/ros1/cmdline.py +++ b/sierra/core/ros1/cmdline.py @@ -1,18 +1,6 @@ # Copyright 2021 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see ` using :term:`ROS1`. diff --git a/sierra/core/ros1/generators.py b/sierra/core/ros1/generators.py index 9e5d9e05..dce1e82f 100644 --- a/sierra/core/ros1/generators.py +++ b/sierra/core/ros1/generators.py @@ -1,18 +1,6 @@ # Copyright 2021 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see `. """ diff --git a/sierra/core/variables/exp_setup.py b/sierra/core/variables/exp_setup.py index 812384ec..bcf5b9c7 100644 --- a/sierra/core/variables/exp_setup.py +++ b/sierra/core/variables/exp_setup.py @@ -1,18 +1,6 @@ # Copyright 2021 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see str: class ExecEnvChecker(platform.ExecEnvChecker): def __init__(self, cmdopts: types.Cmdopts) -> None: super().__init__(cmdopts) + self.logger = logging.getLogger('platform.argos') def __call__(self) -> None: keys = ['ARGOS_PLUGIN_PATH'] @@ -277,12 +266,15 @@ def __call__(self) -> None: # Check ARGoS version stdout = proc.stdout.decode('utf-8') stderr = proc.stderr.decode('utf-8') - res = re.search(r'beta[0-9]+', stdout) + res = re.search(r'[0-9]+.[0-9]+.[0-9]+-beta[0-9]+', stdout) assert res is not None, \ f"ARGOS_VERSION not in stdout: stdout='{stdout}',stderr='{stderr}'" + self.logger.trace("Parsed ARGOS_VERSION: %s", # type: ignore + res.group(0)) + version = packaging.version.parse(res.group(0)) - min_version = packaging.version.parse(config.kARGoS['min_version']) + min_version = config.kARGoS['min_version'] assert version >= min_version,\ f"ARGoS version {version} < min required {min_version}" diff --git a/sierra/plugins/platform/argos/variables/__init__.py b/sierra/plugins/platform/argos/variables/__init__.py index 8fd05bcd..24b09aa8 100644 --- a/sierra/plugins/platform/argos/variables/__init__.py +++ b/sierra/plugins/platform/argos/variables/__init__.py @@ -1,18 +1,6 @@ # Copyright 2022 John Harwell, All rights reserved. # -# This file is part of SIERRA. -# -# SIERRA is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# SIERRA is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# SIERRA. If not, see