Merge pull request #248 from bsipocz/MAINT_mixbag_changes

MAINT: mixbag changes

Author: bsipocz

.circleci/config.yml

@@ -1,40 +1,29 @@
 version: 2.1
 
-
 jobs:
+
   build-docs:
     docker:
-      - image: cimg/python:3.12
+      - image: cimg/python:3.13-node
+
     steps:
       - checkout
 
-      - run:
-          name: Install Node.js
-          command: |
-            curl -fsSL https://deb.nodesource.com/setup_22.x | sudo -E bash -
-            sudo apt-get install -y nodejs
-
-      - run:
-          name: Install mystmd
-          command: |
-            npm install mystmd
-
       - run:
           name: Install Python dependencies
           command: |
             python -m pip install --upgrade pip tox
 
       - run:
-          name: Build documentation
+          name: Build HTML rendering of notebooks
           no_output_timeout: 60m
           environment:
             # Ensure this is same as store_artifacts path below
             DOCS_PATH: _build/html
           command: |
             export BASE_URL="/output/job/$CIRCLE_WORKFLOW_JOB_ID/artifacts/0/$DOCS_PATH"
             export OMP_NUM_THREADS=1
-            python -m tox -e py312-buildhtml
-
+            python -m tox -e py313-buildhtml
 
       - store_artifacts:
           path: _build/html

.mailmap

@@ -0,0 +1,7 @@
+Brigitta Sipőcz <bsipocz@gmail.com>
+Brigitta Sipőcz <bsipocz@gmail.com> <b.sipocz@gmail.com>
+Jessica Krick <jkrick@caltech.edu>
+Tiffany Meshkat <meshkat@ipac.caltech.edu> <meshkat@meshkat.ipac.caltech.edu>
+Tiffany Meshkat <meshkat@ipac.caltech.edu> <meshkat@admins-MBP.attlocal.net>
+Tiffany Meshkat <meshkat@ipac.caltech.edu> <tiffanymeshkat@gmail.com>
+Vandana Desai <vandesai@gmail.com>

myst.yml

@@ -14,6 +14,8 @@ project:
   settings:
     output_matplotlib_strings: remove
   error_rules:
+     - rule: reference-target-resolves
+       severity: error
      - rule: link-resolves
        severity: ignore
        keys:

tox.ini

@@ -33,6 +33,8 @@ deps =
     oldestdeps: sep==1.4.0
     oldestdeps: pyvo==1.5.0
     oldestdeps: pandas==1.5.2
+    # Oldest lsdb is not compatible with the versions above, we skip lsdb notebooks for oldestdeps job
+    # oldestdeps: lsdb==0.6.6
 
     devdeps: astropy>0.0.dev0
     devdeps: git+https://github.com/astropy/pyvo.git#egg=pyvo
@@ -67,13 +69,13 @@ commands =
     # Make a list of all the tutorials to be reused in multiple filtering commands below
     bash -c 'find tutorials -name "*md" | xargs grep kernelspec: | awk -F :kernelspec: "{print \$1}" > all_tutorials'
 
-    # Make a list of the tutorials changed, we only need this in CI. Also deal with grep's non-zero exit code.
-    bash -c 'if [[ $CI == true ]]; then git fetch origin main --depth=1; git diff origin/main --name-only tutorials | grep ".md" || true; fi > changed_tutorials'
+    # Make a list of the tutorials changed, we only need this in CI. Also deal with grep's non-zero exit code. Deleted files are ignored.
+    bash -c 'if [[ $CI == true ]]; then git fetch origin main --depth=1; git diff origin/main --name-only --diff-filter=d tutorials | (grep ".md" || true); fi > changed_tutorials'
 
-    # We only skip testing untouched tutorials in PRs; in cron and dispatch all should be tested
-    !buildhtml: bash -c 'if [[ $GITHUB_EVENT_NAME == pull_request && -z "$(grep force_run:all_tests ${GITHUB_EVENT_PATH})" ]]; then cat changed_tutorials; else cat all_tutorials; fi | grep -vf ignore_testing | xargs jupytext --to notebook '
+    # We only skip testing untouched tutorials in PRs; in cron and dispatch all should be tested. Make sure we don't jupytext non-notebook files.
+    !buildhtml: bash -c 'if [[ $GITHUB_EVENT_NAME == pull_request && -z "$(grep force_run:all_tests ${GITHUB_EVENT_PATH})" ]]; then grep -f changed_tutorials all_tutorials; else cat all_tutorials; fi | grep -vf ignore_testing | xargs jupytext --to notebook '
 
-    !buildhtml: bash -c "echo 'Notebooks ignored (not tested/executed) in this job:\n'; cat ignore_testing"
+    !buildhtml: bash -c "echo 'Notebooks ignored (not tested/executed) in this job:\n'; cat ignore_testing | sort | uniq"
     !buildhtml: pytest --nbval-lax -vv --suppress-no-test-exit-code --durations=10 tutorials
 
     # We don't want to execute in rendering the ones we ignore for testing
@@ -85,7 +87,7 @@ commands =
     # sed -i needs a bit of hacky conditional on ubuntu to cover the case of an empty ignore
     buildhtml: bash -c 'if [ -s ignore_execute ]; then for name in $(cat ignore_execute | sort| uniq); do if [ -z "$(head -n 20 ${name}| grep execute:)" ]; then sed -i -e "s|kernelspec:|execute:\n  skip: true\nkernelspec:|g" ${name}; fi; done;fi'
 
-    buildhtml: bash -c "echo 'Notebooks ignored (not tested/executed) in this job:\n'; cat ignore_execute"
+    buildhtml: bash -c "echo 'Notebooks ignored (not tested/executed) in this job:\n'; cat ignore_execute | sort | uniq"
 
     # Using srtict so we fail with trackbacks and debug mode to have a richer log
     # For full build we disable parallel runs to easy server load

tutorials/cosmodc2/cosmoDC2_TAP_access.md

@@ -10,8 +10,6 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-execution:
-  timeout: 2600
 ---
 
 # Querying the CosmoDC2 Mock v1 Catalogs