Merge pull request #162 from bsipocz/MAINT_using_strict

bsipocz · web-flow · commit d8c84298f740 · 2025-10-31T09:57:18.000-07:00
diff --git a/myst.yml b/myst.yml
@@ -13,6 +13,12 @@ project:
       url: https://mybinder.org
   settings:
     output_matplotlib_strings: remove
+  error_rules:
+     - rule: link-resolves
+       severity: ignore
+       keys:
+         # These link resolve in the browser but generates did not resolve and 403 for the build
+         - https://irsa.ipac.caltech.edu/cgi-bin/Gator/nph-scan?projshort=SPITZER
 extends:
   - toc.yml
 site:
diff --git a/tox.ini b/tox.ini
@@ -38,7 +38,7 @@ deps =
     devdeps: git+https://github.com/astropy/pyvo.git#egg=pyvo
     devdeps: git+https://github.com/astropy/astroquery.git#egg=astroquery
 
-allowlist_externals = bash, jupyter-book
+allowlist_externals = bash
 
 
 install_command =
@@ -65,16 +65,17 @@ commands =
     buildhtml: bash -c 'cat ignore_tutorials/ignore_rendering_execution >> ignore_testing'
 
     # We only want to run CI in PRs for the notebooks we touched
-    !buildhtml: bash -c 'if [[ $GITHUB_EVENT_NAME == pull_request && -z "$(grep force_run:all_tests ${GITHUB_EVENT_PATH})" ]]; then git fetch origin main --depth=1; git diff origin/main --name-only tutorials | grep .md; else find tutorials -name "*.md"; fi | grep -vf ignore_testing/ignore_testing | xargs jupytext --to notebook '
+    !buildhtml: bash -c 'if [[ $GITHUB_EVENT_NAME == pull_request && -z "$(grep force_run:all_tests ${GITHUB_EVENT_PATH})" ]]; then git fetch origin main --depth=1; git diff origin/main --name-only tutorials | grep .md; else find tutorials -name "*.md"; 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: pytest --nbval-lax -vv --suppress-no-test-exit-code --durations=10 tutorials
 
     # sed -i needs a bit of hacky conditional on ubuntu to cover the case of an empty ignore
     buildhtml: bash -c "find tutorials -name '*md' | grep -f ignore_testing | sort | uniq > ignore_execute; if [ -s ignore_execute ]; then cat ignore_execute | xargs -n 1 sed -i -e 's|name: python3|name: python3\nskip_execution: true|g';fi"
 
-    # Status check is a workaround until https://github.com/jupyter-book/mystmd/issues/2113 is fixed
-    buildhtml: bash -c "jupyter-book build --execute --html 2>&1 | tee /tmp/mystbuild.log"
-    buildhtml: bash -c "if grep -q 'Traceback .most recent call last.' /tmp/mystbuild.log; then exit 1; fi"
+    buildhtml: bash -c "echo 'Notebooks ignored (not tested/executed) in this job:\n'; cat ignore_execute"
+    # Using srtict so we fail with trackbacks and debug mode to have a richer log
+    buildhtml: bash -c "npx myst build --execute --html --strict -d"
 
 pip_pre =
     predeps: true
diff --git a/tutorials/cloud_access/cloud-access-intro.md b/tutorials/cloud_access/cloud-access-intro.md
@@ -11,6 +11,7 @@ kernelspec:
   name: python3
 ---
 
+(cloud-access-intro)=
 # IRSA cloud access introduction
 
 This is the introductory tutorial demonstrating basic python access to the IRSA-curated images and catalogs available in AWS S3 cloud storage buckets.
diff --git a/tutorials/firefly/NEOWISE_light_curve_demo.md b/tutorials/firefly/NEOWISE_light_curve_demo.md
@@ -37,9 +37,9 @@ For documentation on the firefly client visit https://caltech-ipac.github.io/fir
 
 ## Imports
 
-- *firefly_client FireflyClient* - Python API to Firefly for displaying tables, images and charts
-- *astropy.utils.data* for downloading the catalog data via TAP query
-- *urllib.parse* for converting regular query string to url-safe string
+- `firefly_client FireflyClient` - Python API to Firefly for displaying tables, images and charts
+- `astropy.utils.data` for downloading the catalog data via TAP query
+- `urllib.parse` for converting regular query string to url-safe string
 
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
diff --git a/tutorials/firefly/SEDs_in_Firefly.md b/tutorials/firefly/SEDs_in_Firefly.md
@@ -84,7 +84,7 @@ import pyvo
 
 +++
 
-From [Figure 10](https://iopscience.iop.org/article/10.3847/1538-3881/ace32f#ajace32ff10) of the referenced paper, pick the source in the upper right corner (J052736.37+344940.6):
+From [Figure 10](https://doi.org/10.3847/1538-3881/ace32f#ajace32ff10) of the referenced paper, pick the source in the upper right corner (J052736.37+344940.6):
 
 ```{code-cell} ipython3
 target = SkyCoord(ra="05h27m36.37s", dec="+34d49m40.6s")
diff --git a/tutorials/irsa-sia-examples/sia_2mass_allsky.md b/tutorials/irsa-sia-examples/sia_2mass_allsky.md
@@ -47,14 +47,14 @@ https://irsa.ipac.caltech.edu/docs/program_interface/api_images.html
 
 ## Imports
 
-- *pyvo* for querying IRSA's 2MASS SIA service
-- *astropy.coordinates* for defining coordinates
-- *astropy.nddata* for creating an image cutout
-- *astropy.wcs* for interpreting the World Coordinate System header keywords of a fits file
-- *astropy.units* for attaching units to numbers passed to the SIA service
-- *matplotlib.pyplot* for plotting
-- *astropy.utils.data* for downloading files
-- *astropy.io* to manipulate FITS files
+- `pyvo` for querying IRSA's 2MASS SIA service
+- `astropy.coordinates` for defining coordinates
+- `astropy.nddata` for creating an image cutout
+- `astropy.wcs` for interpreting the World Coordinate System header keywords of a fits file
+- `astropy.units` for attaching units to numbers passed to the SIA service
+- `matplotlib.pyplot` for plotting
+- `astropy.utils.data` for downloading files
+- `astropy.io` to manipulate FITS files
 
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
diff --git a/tutorials/irsa-sia-examples/sia_allwise_atlas.md b/tutorials/irsa-sia-examples/sia_allwise_atlas.md
@@ -48,14 +48,14 @@ https://irsa.ipac.caltech.edu/docs/program_interface/api_images.html
 
 ## Imports
 
-- *pyvo* for querying IRSA's AllWISE Atlas SIA service
-- *astropy.coordinates* for defining coordinates
-- *astropy.nddata* for creating an image cutout
-- *astropy.wcs* for interpreting the World Coordinate System header keywords of a fits file
-- *astropy.units* for attaching units to numbers passed to the SIA service
-- *matplotlib.pyplot* for plotting
-- *astropy.utils.data* for downloading files
-- *astropy.io* to manipulate FITS files
+- `pyvo` for querying IRSA's AllWISE Atlas SIA service
+- `astropy.coordinates` for defining coordinates
+- `astropy.nddata` for creating an image cutout
+- `astropy.wcs` for interpreting the World Coordinate System header keywords of a fits file
+- `astropy.units` for attaching units to numbers passed to the SIA service
+- `matplotlib.pyplot` for plotting
+- `astropy.utils.data` for downloading files
+- `astropy.io` to manipulate FITS files
 
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
diff --git a/tutorials/irsa-sia-examples/sia_cosmos.md b/tutorials/irsa-sia-examples/sia_cosmos.md
@@ -47,14 +47,14 @@ https://irsa.ipac.caltech.edu/docs/program_interface/api_images.html
 
 ## Imports
 
-- *pyvo* for querying IRSA's COSMOS SIA service
-- *astropy.coordinates* for defining coordinates
-- *astropy.nddata* for creating an image cutout
-- *astropy.wcs* for interpreting the World Coordinate System header keywords of a fits file
-- *astropy.units* for attaching units to numbers passed to the SIA service
-- *matplotlib.pyplot* for plotting
-- *astropy.utils.data* for downloading files
-- *astropy.io* to manipulate FITS files
+- `pyvo` for querying IRSA's COSMOS SIA service
+- `astropy.coordinates` for defining coordinates
+- `astropy.nddata` for creating an image cutout
+- `astropy.wcs` for interpreting the World Coordinate System header keywords of a fits file
+- `astropy.units` for attaching units to numbers passed to the SIA service
+- `matplotlib.pyplot` for plotting
+- `astropy.utils.data` for downloading files
+- `astropy.io` to manipulate FITS files
 
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
diff --git a/tutorials/irsa-sia-examples/siav2_seip.md b/tutorials/irsa-sia-examples/siav2_seip.md
@@ -50,14 +50,14 @@ https://irsa.ipac.caltech.edu/docs/program_interface/api_images.html
 
 ## Imports
 
-- *pyvo* for querying IRSA's SEIP SIA service
-- *astropy.coordinates* for defining coordinates
-- *astropy.nddata* for creating an image cutout
-- *astropy.wcs* for interpreting the World Coordinate System header keywords of a fits file
-- *astropy.units* for attaching units to numbers passed to the SIA service
-- *matplotlib.pyplot* for plotting
-- *astropy.utils.data* for downloading files
-- *astropy.io* to manipulate FITS files
+- `pyvo` for querying IRSA's SEIP SIA service
+- `astropy.coordinates` for defining coordinates
+- `astropy.nddata` for creating an image cutout
+- `astropy.wcs` for interpreting the World Coordinate System header keywords of a fits file
+- `astropy.units` for attaching units to numbers passed to the SIA service
+- `matplotlib.pyplot` for plotting
+- `astropy.utils.data` for downloading files
+- `astropy.io` to manipulate FITS files
 
 ```{code-cell} ipython3
 # Uncomment the next line to install dependencies if needed.
diff --git a/tutorials/parquet-catalog-demos/irsa-hats-with-lsdb.md b/tutorials/parquet-catalog-demos/irsa-hats-with-lsdb.md
@@ -326,7 +326,7 @@ The rationale for selecting these columns is as follows:
 ztf_schema_df[ztf_schema_df.name.isin(ztf_columns)]
 ```
 
-For a quality cut, we apply the following filter on the number of good epochs (from [Coughlin et al. 2021](https://academic.oup.com/mnras/article/505/2/2954/6284767) section 2):
+For a quality cut, we apply the following filter on the number of good epochs (from {cite}`doi.org/10.1093/mnras/stab1502`) section 2):
 
 ```{code-cell} ipython3
 quality_filters = [
diff --git a/tutorials/parquet-catalog-demos/neowise-source-table-lightcurves.md b/tutorials/parquet-catalog-demos/neowise-source-table-lightcurves.md
@@ -11,6 +11,7 @@ kernelspec:
   name: python3
 ---
 
+(neowise-lightcurves-parquet)=
 # Make Light Curves from NEOWISE Single-exposure Source Table
 
 +++
diff --git a/tutorials/parquet-catalog-demos/neowise-source-table-strategies.md b/tutorials/parquet-catalog-demos/neowise-source-table-strategies.md
@@ -110,9 +110,9 @@ A fully-worked example is shown in the light curve notebook linked below.
 
 ### 1.3 See also
 
-- [IRSA Cloud Access Intro](https://irsa.ipac.caltech.edu/docs/notebooks/cloud-access-intro.html)
-- [AllWISE Source Catalog Demo](https://irsa.ipac.caltech.edu/docs/notebooks/wise-allwise-catalog-demo.html)
-- [Make Light Curves from NEOWISE Single-exposure Source Table](https://irsa.ipac.caltech.edu/docs/notebooks/neowise-source-table-lightcurves.html)
+- [](#cloud-access-intro)
+- [](#allwise-source-catalog-parquet)
+- [](#neowise-lightcurves-parquet)
 
 +++
 
diff --git a/tutorials/parquet-catalog-demos/wise-allwise-catalog-demo.md b/tutorials/parquet-catalog-demos/wise-allwise-catalog-demo.md
@@ -11,6 +11,7 @@ kernelspec:
   name: python3
 ---
 
+(allwise-source-catalog-parquet)=
 # Analyzing cloud-hosted AllWISE Source Catalog in Parquet format
 
 +++
@@ -29,7 +30,7 @@ kernelspec:
 
 ## Introduction
 
-This notebook demonstrates access to the [HEALPix](https://ui.adsabs.harvard.edu/abs/2005ApJ...622..759G/abstract)-partitioned (order 5), [Apache Parquet](https://parquet.apache.org/) version of the [AllWISE Source Catalog](https://wise2.ipc.caltech.edu/docs/release/allwise/expsup/sec1_3.html#src_cat).
+This notebook demonstrates access to the [HEALPix](https://ui.adsabs.harvard.edu/abs/2005ApJ...622..759G/abstract)-partitioned (order 5), [Apache Parquet](https://parquet.apache.org/) version of the [AllWISE Source Catalog](https://wise2.ipac.caltech.edu/docs/release/allwise/expsup/sec1_3.html#src_cat).
 The catalog is available through the [AWS Open Data](https://aws.amazon.com/opendata) program, as part of the [NASA Open-Source Science Initiative](https://science.nasa.gov/open-science-overview).
 
 Parquet is convenient for large astronomical catalogs in part because the storage format supports efficient database-style queries on the files themselves, without having to load the catalog into a database (or into memory) first.
diff --git a/tutorials/spherex/spherex_intro.md b/tutorials/spherex/spherex_intro.md
@@ -36,7 +36,7 @@ SPHEREx is a NASA Astrophysics Medium Explorer mission that launched in March 20
 
 The community will also mine SPHEREx data and combine it with synergistic data sets to address a variety of additional topics in astrophysics.
 
-More information is available in the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR_v1.0.pdf).
+More information is available in the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
 
 +++
 
@@ -330,7 +330,7 @@ Now let's take a look at some header keywords that provide information about how
 spectral_image_header['L2 N_*']
 ```
 
-There are 14 flags in total. Typically, most of the pixels are identified as SOURCE pixels, which are pixels mapped to a known source. The remaining flags are described in Table 8 of the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/spherex_explanatory_supplement.pdf).
+There are 14 flags in total. Typically, most of the pixels are identified as SOURCE pixels, which are pixels mapped to a known source. The remaining flags are described in Table 8 of the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
 
 +++
 
