From 79f2599a9e45f89ffb1891e1da87c912b6c81757 Mon Sep 17 00:00:00 2001 From: Jonathan Sick Date: Mon, 18 Jan 2021 13:19:38 -0500 Subject: [PATCH 01/10] Delete requirements.txt No longer needed with Documenteer inside the Rubin Conda environment (RFC-733). --- requirements.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index eed9c588..00000000 --- a/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -documenteer[pipelines]>=0.5.0,<0.6.0 From 9693800f98e0f1aabbc4f803b488f05457dd19b8 Mon Sep 17 00:00:00 2001 From: Jonathan Sick Date: Mon, 18 Jan 2021 13:20:52 -0500 Subject: [PATCH 02/10] Delete the Travis file Travis is no longer needed; moving to GitHub Actions to provide the check for PRs. --- .travis.yml | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 97e4d7a4..00000000 --- a/.travis.yml +++ /dev/null @@ -1,12 +0,0 @@ -# This is currently a no-op Travis configuration so that the GitHub repo -# can get a Checks API callback to ensure that branches are up-to-date before -# merging. Eventually we could add static linting. -# -# The build itself is done by: -# https://ci.lsst.codes/blue/organizations/jenkins/sqre%2Finfra%2Fdocumenteer/activity - -language: python -python: - - "3.6" -script: - - "true" From 89a2c950daadb9f11c5ee678cb11db039f272026 Mon Sep 17 00:00:00 2001 From: Jonathan Sick Date: Mon, 18 Jan 2021 13:23:16 -0500 Subject: [PATCH 03/10] Migrated to Documenteer 0.6 config API See https://documenteer.lsst.io/pipelines/configuration.html for documentation. --- conf.py | 38 +++++++------------------------------- 1 file changed, 7 insertions(+), 31 deletions(-) diff --git a/conf.py b/conf.py index 70726b05..66665778 100644 --- a/conf.py +++ b/conf.py @@ -1,37 +1,13 @@ """Sphinx configurations for pipeline_lsst_io. -These configurations are centrally defined in Documenteer -(https://github.com/lsst-sqre/documenteer). +These configurations are centrally defined in Documenteer: +https://documenteer.lsst.io/pipelines/configuration.html """ -from documenteer.sphinxconfig.stackconf import \ - build_pipelines_lsst_io_configs +from documenteer.conf.pipelines import * # noqa: F403 -globals().update(build_pipelines_lsst_io_configs( - project_name='LSST Science Pipelines', -)) - -# Patch EUPS tag subsitutions -rst_epilog = """ - -.. |eups-tag| replace:: v21_0_0 -.. |eups-tag-mono| replace:: ``v21_0_0`` -.. |eups-tag-bold| replace:: **v21_0_0** -""" - -# Patch EUPS and Git tag context for Jinja templating -jinja_contexts = { - "default": { - "release_eups_tag": "v21_0_0", - "release_git_ref": "21.0.0", - "version": "v21_0_0", - "release": "v21_0_0", - "scipipe_conda_ref": "21.0.0", - "pipelines_demo_ref": "21.0.0", - "newinstall_ref": "21.0.0", - } -} - -import matplotlib.sphinxext.plot_directive -extensions.remove(matplotlib.sphinxext.plot_directive.__name__) +project_name = "LSST Science Pipelines" +html_theme_options["logotext"] = project_name # noqa: F405 +html_title = project_name +html_short_title = project_name From d16dfff92e55f3778fd1b17f19868ed48ccde02b Mon Sep 17 00:00:00 2001 From: Jonathan Sick Date: Tue, 19 Jan 2021 11:55:05 -0500 Subject: [PATCH 04/10] Add null GitHub Actions workflow This will be useful for setting up branch protections to ensure the branch is up-to-date. However, hopefully we can add more useful linting in the future. --- .github/workflows/ci.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 .github/workflows/ci.yaml diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 00000000..5f85b22a --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,12 @@ +name: Empty check for branch protection + +on: + - push + - pull_request + +jobs: + + null_check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 From f79c2f98f9fbbc492e1f2da2473bb579d2d3b5ac Mon Sep 17 00:00:00 2001 From: Jonathan Sick Date: Wed, 14 Apr 2021 09:50:00 -0400 Subject: [PATCH 05/10] Undo automodapi autodoc enhancements Undo the automodapi autodoc enhancements that are incompatible with pybind11 properties. Essentially this restores the built-in getattr as the attr getter for "type" rather than https://github.com/astropy/sphinx-automodapi/blob/b68a5f3c6805d7c5d0eaa55fff1ff84cc671baf0/sphinx_automodapi/autodoc_enhancements.py#L15 --- conf.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/conf.py b/conf.py index 66665778..08c7bd4b 100644 --- a/conf.py +++ b/conf.py @@ -11,3 +11,11 @@ html_theme_options["logotext"] = project_name # noqa: F405 html_title = project_name html_short_title = project_name + + +def setup(app): + # Undo the automodapi autodoc enhancements that are incompatible with + # pybind11 properties. Essentially this restores the built-in getattr + # as the attr getter for "type" rather than + # https://github.com/astropy/sphinx-automodapi/blob/b68a5f3c6805d7c5d0eaa55fff1ff84cc671baf0/sphinx_automodapi/autodoc_enhancements.py#L15 + app.add_autodoc_attrgetter(type, getattr) From b2fc3f8d91be44904868dbb7a9c8647ce73b1f1f Mon Sep 17 00:00:00 2001 From: Kian-Tat Lim Date: Wed, 14 Apr 2021 21:23:25 -0700 Subject: [PATCH 06/10] Add eupspkg.cfg.sh. --- ups/eupspkg.cfg.sh | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 ups/eupspkg.cfg.sh diff --git a/ups/eupspkg.cfg.sh b/ups/eupspkg.cfg.sh new file mode 100644 index 00000000..77fdb25b --- /dev/null +++ b/ups/eupspkg.cfg.sh @@ -0,0 +1,3 @@ +build() { + stack-docs build +} From 4a16340149598745d9261a272ed78beeace8fe82 Mon Sep 17 00:00:00 2001 From: Kian-Tat Lim Date: Thu, 22 Apr 2021 09:33:12 -0700 Subject: [PATCH 07/10] Compensate for SIP on macOS. --- ups/eupspkg.cfg.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ups/eupspkg.cfg.sh b/ups/eupspkg.cfg.sh index 77fdb25b..60f228a3 100644 --- a/ups/eupspkg.cfg.sh +++ b/ups/eupspkg.cfg.sh @@ -1,3 +1,8 @@ build() { + # macOS SIP swallows DYLD_LIBRARY_PATH so export the duplicate in + # LSST_LIBRARY_PATH + if [[ -z $DYLD_LIBRARY_PATH ]]; then + export DYLD_LIBRARY_PATH=$LSST_LIBRARY_PATH + fi stack-docs build } From e373d833c7d30dc8a47af37564c1fba622c889f6 Mon Sep 17 00:00:00 2001 From: Kian-Tat Lim Date: Thu, 22 Apr 2021 18:34:02 -0700 Subject: [PATCH 08/10] Minimize installation size. --- ups/eupspkg.cfg.sh | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/ups/eupspkg.cfg.sh b/ups/eupspkg.cfg.sh index 60f228a3..6c21f8e6 100644 --- a/ups/eupspkg.cfg.sh +++ b/ups/eupspkg.cfg.sh @@ -6,3 +6,20 @@ build() { fi stack-docs build } + +install() { + clean_old_install + mkdir -p "$PREFIX" + cp -a \ + _build.log \ + _build.sh \ + _build.tags \ + conf.py \ + COPYRIGHT \ + LICENSE \ + README.md "$PREFIX" + cd "$reldir" + if [[ -d "ups" && ! -d "$PREFIX/ups" ]]; then + install_ups + fi +} From 120c5a606ca5f120fc9a56f3e95ed8e2f4f41362 Mon Sep 17 00:00:00 2001 From: Kian-Tat Lim Date: Fri, 23 Apr 2021 07:39:31 -0700 Subject: [PATCH 09/10] Fix v21 release notes. --- releases/v21_0_0.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/releases/v21_0_0.rst b/releases/v21_0_0.rst index 3659575b..0eb6bfd7 100644 --- a/releases/v21_0_0.rst +++ b/releases/v21_0_0.rst @@ -57,7 +57,7 @@ Major New Features Beta release of Generation 3 Middleware --------------------------------------- -Reaching schema stability in this release, the Gen3 butler can now support Science Pipelines development. See :ref:`release-v21-0-0-deprecate-gen2` for more information on the planned deprecation of Generation 2 middleware. Interested parties may find more info at :ref:`daf_butler ` and :ref:`pipe_base `. +Reaching schema stability in this release, the Gen3 butler can now support Science Pipelines development. See :ref:`release-v21-0-0-deprecate-gen2` for more information on the planned deprecation of Generation 2 middleware. Interested parties may find more info at :ref:`daf_butler ` and :ref:`pipe_base `. A general release of Generation 3 Middleware is expected with the next release v22.0.0. .. _release-v21-0-0-kht: @@ -65,7 +65,7 @@ A general release of Generation 3 Middleware is expected with the next release v Task to mask streak-like artifacts ---------------------------------- -This release adds the `MaskStreaksTask` to :ref:`pipe_tasks `, which finds and masks streaks and other straight lines in image data. +This release adds the `MaskStreaksTask` to :ref:`pipe_tasks `, which finds and masks streaks and other straight lines in image data. It uses the Kernel Hough Transform (KHT) `(Fernandes and Oliveira 2007) `_ implemented in the `kht `_, package which was also added to the Science Pipelines. It can be turned on during coaddition with `CompareWarpAssembleCoaddTask` with the config parameter `doFilterMorphological`. @@ -130,9 +130,9 @@ For more information, refer to :jira:`RFC-736`. .. _release-v21-0-0-pipelines_check: Addition of the pipelines_check package ------------------------------------ +--------------------------------------- -The new :ref:`pipelines_check ` package replaces `lsst_dm_stack_demo`, which relied on the now :ref:`release-v21-0-0-remove-obs_sdss`. This new package demonstrates the processing of a single CCD with the Science Pipelines. It contains input files and astrometric reference catalogs needed to process the data from a single HSC detector. Its main purpose is to check that the pipeline infrastructure is working correctly. +The new :ref:`pipelines_check ` package replaces `lsst_dm_stack_demo`, which relied on the now :ref:`removed obs_sdss`. This new package demonstrates the processing of a single CCD with the Science Pipelines. It contains input files and astrometric reference catalogs needed to process the data from a single HSC detector. Its main purpose is to check that the pipeline infrastructure is working correctly. .. _release-v21-0-0-remove-obs_sdss: From 6255257da663aab2d384ccf83685da851b51e3c4 Mon Sep 17 00:00:00 2001 From: Kian-Tat Lim Date: Fri, 23 Apr 2021 09:17:48 -0700 Subject: [PATCH 10/10] Remove bad pipelines_check reference. --- releases/v21_0_0.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/releases/v21_0_0.rst b/releases/v21_0_0.rst index 0eb6bfd7..f137c331 100644 --- a/releases/v21_0_0.rst +++ b/releases/v21_0_0.rst @@ -132,7 +132,7 @@ For more information, refer to :jira:`RFC-736`. Addition of the pipelines_check package --------------------------------------- -The new :ref:`pipelines_check ` package replaces `lsst_dm_stack_demo`, which relied on the now :ref:`removed obs_sdss`. This new package demonstrates the processing of a single CCD with the Science Pipelines. It contains input files and astrometric reference catalogs needed to process the data from a single HSC detector. Its main purpose is to check that the pipeline infrastructure is working correctly. +The new `pipelines_check` package replaces `lsst_dm_stack_demo`, which relied on the now :ref:`removed obs_sdss`. This new package demonstrates the processing of a single CCD with the Science Pipelines. It contains input files and astrometric reference catalogs needed to process the data from a single HSC detector. Its main purpose is to check that the pipeline infrastructure is working correctly. .. _release-v21-0-0-remove-obs_sdss: