From 2d369a21a8fdb409c3db03282d0e40a3c7b71a12 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 7 Oct 2024 21:33:59 +0000 Subject: [PATCH 01/12] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v5.0.0) - [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](https://github.com/codespell-project/codespell/compare/v2.2.6...v2.3.0) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c1ead0..055ce21 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ ci: autoupdate_schedule: 'quarterly' repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v5.0.0 hooks: - id: check-added-large-files args: ['--maxkb=1000'] @@ -15,7 +15,7 @@ repos: - id: no-commit-to-branch args: [--branch, main] - repo: https://github.com/codespell-project/codespell - rev: v2.2.6 + rev: v2.3.0 hooks: - id: codespell files: ^.*\.(md|rst|yml)$ \ No newline at end of file From d1c46726ef49153a2faa18d67ab591847a5327e4 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Thu, 2 Jan 2025 15:01:25 -0700 Subject: [PATCH 02/12] Fixed typo --- CODE_OF_CONDUCT.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 2cab80d..7e87d57 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -21,7 +21,7 @@ productive environment that enriches the surrounding community. We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, +identity and expression, level of experience, education, socioeconomic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. From 593e7d8395ce3990cd07659285b4e4fc7668fb50 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Jan 2025 21:06:45 +0000 Subject: [PATCH 03/12] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/markdownlint/markdownlint: v0.11.0 → v0.12.0](https://github.com/markdownlint/markdownlint/compare/v0.11.0...v0.12.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index db539b8..ab285e9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: - id: codespell files: ^.*\.(md|rst|yml)$ - repo: https://github.com/markdownlint/markdownlint - rev: v0.11.0 + rev: v0.12.0 hooks: - id: markdownlint files: ^.*\.(md)$ \ No newline at end of file From 4a25789eb88f2bdde989f8843d6426db515a688d Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Tue, 11 Mar 2025 15:12:23 -0600 Subject: [PATCH 04/12] Updates from pre-commit update PR --- .gitignore | 3 ++- .mdl_style.rb | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 77c02a2..09ba2e0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ .idea/ -docs/source/build \ No newline at end of file +docs/source/build +docs/build \ No newline at end of file diff --git a/.mdl_style.rb b/.mdl_style.rb index 234a985..3d3a7cf 100644 --- a/.mdl_style.rb +++ b/.mdl_style.rb @@ -4,4 +4,4 @@ exclude_rule 'MD033' # Inline HTML exclude_rule 'MD034' # Bare URL used exclude_rule 'MD036' # Emphasis used instead of a header -rule 'MD013', :line_length => 120, :code_blocks => false, :tables => false \ No newline at end of file +rule 'MD013', :line_length => 120, :ignore_code_blocks => true, :tables => false \ No newline at end of file From cae643b0ef80b4044b83b39cc79ceec2c0050f38 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Tue, 11 Mar 2025 15:37:52 -0600 Subject: [PATCH 05/12] pre-commit check now requires blank line at end of file --- .pre-commit-config.yaml | 2 +- docs/source/data_management/fair_principles.md | 2 +- docs/source/data_management/file_formats/netcdf.md | 2 +- docs/source/data_management/metadata.md | 2 +- docs/source/licensing.md | 3 ++- docs/source/workflows/docker/beginner_guide_to_docker.md | 2 +- docs/source/workflows/docker/containerizing_idl_with_docker.md | 2 +- docs/source/workflows/docker/docker_compose_examples.md | 2 +- docs/source/workflows/docker/export_display_with_docker.md | 2 +- docs/source/workflows/docker/lasp_docker_registry.md | 2 +- docs/source/workflows/docker/lasp_image_registry.md | 2 +- docs/source/workflows/jenkins_job_builder/containerize_jjb.md | 2 +- 12 files changed, 13 insertions(+), 12 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ab285e9..db539b8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: - id: codespell files: ^.*\.(md|rst|yml)$ - repo: https://github.com/markdownlint/markdownlint - rev: v0.12.0 + rev: v0.11.0 hooks: - id: markdownlint files: ^.*\.(md)$ \ No newline at end of file diff --git a/docs/source/data_management/fair_principles.md b/docs/source/data_management/fair_principles.md index 61b1b27..7d835cc 100644 --- a/docs/source/data_management/fair_principles.md +++ b/docs/source/data_management/fair_principles.md @@ -126,4 +126,4 @@ must be well-described to enable replication and/or combination in different set - **NIH** = National Institutes of Health - **NOAA** = National Oceanic and Atmospheric Administration -Credit: Content taken from a Confluence guide written by Anne Wilson, and modified by Shawn Polson in 2019 \ No newline at end of file +Credit: Content taken from a Confluence guide written by Anne Wilson, and modified by Shawn Polson in 2019 diff --git a/docs/source/data_management/file_formats/netcdf.md b/docs/source/data_management/file_formats/netcdf.md index be49adb..6711e6b 100644 --- a/docs/source/data_management/file_formats/netcdf.md +++ b/docs/source/data_management/file_formats/netcdf.md @@ -121,4 +121,4 @@ There are two netCDF data models: * [NetCDF ToolsUI](https://docs.unidata.ucar.edu/netcdf-java/current/userguide/toolsui_ref.html) * [NetCDF Workshop Materials](https://www.unidata.ucar.edu/software/netcdf/workshops/2011/index.html) -Credit: Content taken from a Confluence guide written by Doug Lindholm \ No newline at end of file +Credit: Content taken from a Confluence guide written by Doug Lindholm diff --git a/docs/source/data_management/metadata.md b/docs/source/data_management/metadata.md index be82b40..1bc910e 100644 --- a/docs/source/data_management/metadata.md +++ b/docs/source/data_management/metadata.md @@ -166,4 +166,4 @@ Provenance is often provided as descriptive prose, making machine-readable text - **LEMR** = LASP Extended Metadata Repository - **SPASE** = Space Physics Archive Search and Extract -Credit: Content taken from a Confluence guide written by Anne Wilson and Shawn Polson. \ No newline at end of file +Credit: Content taken from a Confluence guide written by Anne Wilson and Shawn Polson. diff --git a/docs/source/licensing.md b/docs/source/licensing.md index 0ec4506..54e07a7 100644 --- a/docs/source/licensing.md +++ b/docs/source/licensing.md @@ -87,4 +87,5 @@ you’re distributing/producing. * [Choose a license](https://choosealicense.com/) * [Open Source Initiative (OSI)](https://opensource.org/licenses) * [The Turing Way overview of licensing](https://the-turing-way.netlify.app/reproducible-research/licensing) -* [Free and Open Source License Comparison chart](https://en.wikipedia.org/wiki/Comparison_of_free_and_open-source_software_licenses) \ No newline at end of file +* [Free and Open Source License Comparison chart](https://en.wikipedia.org/wiki/Comparison_of_free_and_open-source_software_licenses) +* \ No newline at end of file diff --git a/docs/source/workflows/docker/beginner_guide_to_docker.md b/docs/source/workflows/docker/beginner_guide_to_docker.md index e3e264e..13db679 100644 --- a/docs/source/workflows/docker/beginner_guide_to_docker.md +++ b/docs/source/workflows/docker/beginner_guide_to_docker.md @@ -190,4 +190,4 @@ docker image prune * **ps** = Process Status * **tty** = TeleTYpe (terminal) -*Credit: Content taken from a Confluence guide written by Maxine Hartnett* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Maxine Hartnett* diff --git a/docs/source/workflows/docker/containerizing_idl_with_docker.md b/docs/source/workflows/docker/containerizing_idl_with_docker.md index eb9b6ac..a514816 100644 --- a/docs/source/workflows/docker/containerizing_idl_with_docker.md +++ b/docs/source/workflows/docker/containerizing_idl_with_docker.md @@ -418,4 +418,4 @@ docker container run -e DISPLAY=host.docker.internal:0 idlde_image * **VPN** = Virtual Private Network * **yum** = Yellowdog Updater, Modified -*Credit: Content taken from a Confluence guide written by Steven Mueller* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Steven Mueller* diff --git a/docs/source/workflows/docker/docker_compose_examples.md b/docs/source/workflows/docker/docker_compose_examples.md index f97ac8f..63837b9 100644 --- a/docs/source/workflows/docker/docker_compose_examples.md +++ b/docs/source/workflows/docker/docker_compose_examples.md @@ -359,4 +359,4 @@ And you will need some Flyway migration scripts to build up your DB schema howev * **apk** = Alpine Package Keeper * **pip** = Pip Installs Packages -*Credit: Content taken from a Confluence guide written by Gavin Medley and Maxine Hartnett* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Gavin Medley and Maxine Hartnett* diff --git a/docs/source/workflows/docker/export_display_with_docker.md b/docs/source/workflows/docker/export_display_with_docker.md index 32fc78a..cdec5a8 100644 --- a/docs/source/workflows/docker/export_display_with_docker.md +++ b/docs/source/workflows/docker/export_display_with_docker.md @@ -47,4 +47,4 @@ argument) allows the container access to the host machine X socket. * [Official Docker documentation](https://docs.docker.com/) -*Credit: Content taken from a Confluence guide written by Steven Mueller* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Steven Mueller* diff --git a/docs/source/workflows/docker/lasp_docker_registry.md b/docs/source/workflows/docker/lasp_docker_registry.md index 30ee218..b7528ad 100644 --- a/docs/source/workflows/docker/lasp_docker_registry.md +++ b/docs/source/workflows/docker/lasp_docker_registry.md @@ -167,4 +167,4 @@ WEBSUPPORT ticket or send an email to `web.support@lasp.colorado.edu` * **UI** = User Interface * **URL** = Uniform Resource Locator -*Credit: Content taken from a Confluence guide written by Maxine Hartnett* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Maxine Hartnett* diff --git a/docs/source/workflows/docker/lasp_image_registry.md b/docs/source/workflows/docker/lasp_image_registry.md index 1cb3767..5656fe5 100644 --- a/docs/source/workflows/docker/lasp_image_registry.md +++ b/docs/source/workflows/docker/lasp_image_registry.md @@ -115,4 +115,4 @@ Only the image argument is relevant to the registry pull. * **TIM** = Total Irradiance Monitor * **URL** = Uniform Resource Locator -*Credit: Content taken from a Confluence guide written by Steven Mueller* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Steven Mueller* diff --git a/docs/source/workflows/jenkins_job_builder/containerize_jjb.md b/docs/source/workflows/jenkins_job_builder/containerize_jjb.md index 08f7356..c9cae4b 100644 --- a/docs/source/workflows/jenkins_job_builder/containerize_jjb.md +++ b/docs/source/workflows/jenkins_job_builder/containerize_jjb.md @@ -6,4 +6,4 @@ ## Acronyms -*Credit: Content taken from a Confluence guide written by Steven Mueller* \ No newline at end of file +*Credit: Content taken from a Confluence guide written by Steven Mueller* From ac379cc5bfd5bf811c44941934815ed80b9defc6 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Tue, 11 Mar 2025 15:46:00 -0600 Subject: [PATCH 06/12] squash --- docs/source/licensing.md | 1 - .../docker/containerizing_idl_with_docker.md | 27 ++++++++++++++++--- 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/docs/source/licensing.md b/docs/source/licensing.md index 54e07a7..11a442a 100644 --- a/docs/source/licensing.md +++ b/docs/source/licensing.md @@ -88,4 +88,3 @@ you’re distributing/producing. * [Open Source Initiative (OSI)](https://opensource.org/licenses) * [The Turing Way overview of licensing](https://the-turing-way.netlify.app/reproducible-research/licensing) * [Free and Open Source License Comparison chart](https://en.wikipedia.org/wiki/Comparison_of_free_and_open-source_software_licenses) -* \ No newline at end of file diff --git a/docs/source/workflows/docker/containerizing_idl_with_docker.md b/docs/source/workflows/docker/containerizing_idl_with_docker.md index a514816..ee03765 100644 --- a/docs/source/workflows/docker/containerizing_idl_with_docker.md +++ b/docs/source/workflows/docker/containerizing_idl_with_docker.md @@ -169,7 +169,11 @@ running on the host machine from within the non-IDL container. In this example a container is created from the official `CentOS` image: ```bash -docker container run -it --name=centos_container --rm -v /var/run/docker.sock:/var/run/docker.sock -v /usr/bin/docker:/usr/bin/docker centos bash +docker container run -it \ + --name=centos_container --rm \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v /usr/bin/docker:/usr/bin/docker \ + centos bash ``` This `docker container run` command generates a CentOS container and initiates an interactive connection to that @@ -240,7 +244,12 @@ Now, as in the previous example, spin up a non-IDL container based on the offici additional bind mount for the newly-created data volume: ```bash -docker container run --rm -it --name=centos_container -v /var/run/docker.sock:/var/run/docker.sock -v /usr/bin/docker:/usr/bin/docker -v SharedData:/src centos bash +docker container run --rm -it \ + --name=centos_container \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v /usr/bin/docker:/usr/bin/docker \ + -v SharedData:/src \ + centos bash ``` #### In the Interactive Shell Inside the `CentOS` Container @@ -296,7 +305,12 @@ mounted to the `/src` directory in the container. Now create the non-IDL container named `centos_container`: ```bash -docker container run --rm -it --name=centos_container -v /Users/stmu4541/projects/docker/src:/src -v /var/run/docker.sock:/var/run/docker.sock -v /usr/bin/docker:/usr/bin/docker lentos bash +docker container run --rm -it \ + --name=centos_container \ + -v /Users/stmu4541/projects/docker/src:/src \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v /usr/bin/docker:/usr/bin/docker \ + lentos bash ``` Here, `lentos`, which immediately precedes the bash command specifies the official `centos` image. @@ -315,7 +329,12 @@ Using a Jenkins-based principal container is not significantly different than th latest `CentOS` OS. ```bash -docker container run --name=jenkins -v /var/run/docker.sock:/var/run/docker.sock -v /usr/bin/docker:/usr/bin/docker -p 8080:8080 jenkins/jenkins:lts-centos +docker container run \ + --name=jenkins \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v /usr/bin/docker:/usr/bin/docker \ + -p 8080:8080 \ + jenkins/jenkins:lts-centos ``` Note that a Dockerfile is not required for this simple example since the container is created from the official `CentOS` From ff04653a81e97a2ffe33af275e4062d31ae28c74 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Tue, 11 Mar 2025 15:49:17 -0600 Subject: [PATCH 07/12] squash --- docs/source/workflows/docker/lasp_image_registry.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/source/workflows/docker/lasp_image_registry.md b/docs/source/workflows/docker/lasp_image_registry.md index 5656fe5..bd125e2 100644 --- a/docs/source/workflows/docker/lasp_image_registry.md +++ b/docs/source/workflows/docker/lasp_image_registry.md @@ -78,7 +78,10 @@ docker pull docker-registry.pdmz.lasp.colorado.edu/tsis/dsinteg2_migration Or, the following command: ```bash -docker container run --user root --rm -it --name timDevContainer docker-registry.pdmz.lasp.colorado.edu/tsis/dsinteg2_migration bash +docker container run --user root --rm -it \ + --name timDevContainer \ + docker-registry.pdmz.lasp.colorado.edu/tsis/dsinteg2_migration \ + bash ``` This will launch a container based on the registry `dsinteg2_migration` image and connect to that container with a From 4b160455151b2816feae48fa6ae2beaeb271a53d Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Tue, 11 Mar 2025 15:56:25 -0600 Subject: [PATCH 08/12] squash --- .readthedocs.yaml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index d5a54c7..5e7b963 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,15 +8,20 @@ build: os: "ubuntu-22.04" tools: python: "3.10" + environment: + POETRY_VIRTUALENVS_IN_PROJECT: "true" + POETRY_VIRTUALENVS_CREATE: "true" jobs: post_create_environment: - # Install poetry - # https://python-poetry.org/docs/#installing-manually - python -m pip install poetry post_install: - # Install dependencies with 'docs' dependency group - # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install + - poetry install --only docs # Using the docs dependency group + +python: + install: + - method: poetry + path: . sphinx: - configuration: docs/source/conf.py \ No newline at end of file + configuration: docs/source/conf.py + From 7db6fa1c0e2e4cfc22a717a0c14428f877ebc287 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Thu, 20 Mar 2025 14:17:11 -0600 Subject: [PATCH 09/12] reverting back to original (somewhat working) rtd config --- .readthedocs.yaml | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 5e7b963..d5a54c7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,20 +8,15 @@ build: os: "ubuntu-22.04" tools: python: "3.10" - environment: - POETRY_VIRTUALENVS_IN_PROJECT: "true" - POETRY_VIRTUALENVS_CREATE: "true" jobs: post_create_environment: + # Install poetry + # https://python-poetry.org/docs/#installing-manually - python -m pip install poetry post_install: - - poetry install --only docs # Using the docs dependency group - -python: - install: - - method: poetry - path: . + # Install dependencies with 'docs' dependency group + # https://python-poetry.org/docs/managing-dependencies/#dependency-groups + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install sphinx: - configuration: docs/source/conf.py - + configuration: docs/source/conf.py \ No newline at end of file From 81054317968128aacba88501bef349e5ab38e6ba Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Thu, 20 Mar 2025 14:20:52 -0600 Subject: [PATCH 10/12] squash --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a7e6c09..089ede0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,7 @@ requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" -[tool.poetry] +[project] name = "developer-guide" version = "0.1.0" description = "Guidelines for software developers at LASP" From c58fad93bec6a0b5ad27eb0c7cab6c3da151c57e Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Thu, 20 Mar 2025 14:26:40 -0600 Subject: [PATCH 11/12] squash --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 089ede0..c5c4c84 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,10 +7,10 @@ name = "developer-guide" version = "0.1.0" description = "Guidelines for software developers at LASP" authors = [ - "Matthew Bourque ", - "Keira Brooks ", - "Veronica Martinez ", - "Alex Ware "] + {name = "Matthew Bourque", email = "Matthew.Bourque@lasp.colorado.edu>"}, + {name = "Keira Brooks", email = "Keira.Brooks@lasp.colorado.edu>"}, + {name = "Veronica Martinez", email = "Veronica.Martinez@lasp.colorado.edu>"}, + {name = "Alex Ware", email = "Alex.Ware@lasp.colorado.edu>"}] readme = "README.md" license = "MIT" keywords = ["LASP", "Developer Guide", "Software"] From e8eb47f228ea13ddacf5e3a84000c25a6f74a819 Mon Sep 17 00:00:00 2001 From: Matthew Bourque Date: Thu, 20 Mar 2025 14:29:07 -0600 Subject: [PATCH 12/12] squash --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index c5c4c84..bcacbaa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,9 @@ classifiers = [ "Topic :: Scientific/Engineering", ] +[tool.poetry] +package-mode = false + [tool.poetry.dependencies] myst-parser = "^3.0.1" python = ">=3.9,<4"