Merge pull request #347 from lsst-sqre/tickets/DM-44397/notebook-dire…

…ctories

DM-44397: Run all notebooks in repo directory

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

changelog.d/20240520_113001_danfuchs_notebook_directories.md

@@ -0,0 +1,6 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+- NotebookRunner business now runs all notebooks in a repo, at tht root and in all subdirs recursively, by default.
+- Add `exclude_dirs` option to NotebookRunner business to list directories in which notebooks will not be run.

requirements/dev.txt

@@ -3,10 +3,13 @@
 anyio==4.3.0 \
     --hash=sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8 \
     --hash=sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6
-    # via httpx
+    # via
+    #   -c requirements/main.txt
+    #   httpx
 asgi-lifespan==2.1.0 \
     --hash=sha256:5e2effaf0bfe39829cf2d64e7ecc47c7d86d676a6599f7afba378c31f5e3a308 \
     --hash=sha256:ed840706680e28428c01e14afb3875d7d76d3206f3d5b2f2294e059b5c23804f
+    # via -r requirements/dev.in
 attrs==23.2.0 \
     --hash=sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30 \
     --hash=sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1
@@ -15,6 +18,7 @@ certifi==2024.2.2 \
     --hash=sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f \
     --hash=sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1
     # via
+    #   -c requirements/main.txt
     #   httpcore
     #   httpx
     #   requests
@@ -113,11 +117,14 @@ charset-normalizer==3.3.2 \
     --hash=sha256:fb69256e180cb6c8a894fee62b3afebae785babc1ee98b81cdf68bbca1987f33 \
     --hash=sha256:fd1abc0d89e30cc4e02e4064dc67fcc51bd941eb395c502aac3ec19fab46b519 \
     --hash=sha256:ff8fa367d09b717b2a17a052544193ad76cd49979c805768879cb63d9ca50561
-    # via requests
+    # via
+    #   -c requirements/main.txt
+    #   requests
 click==8.1.7 \
     --hash=sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28 \
     --hash=sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de
     # via
+    #   -c requirements/main.txt
     #   click-log
     #   scriv
 click-log==0.4.0 \
@@ -177,7 +184,9 @@ coverage==7.5.1 \
     --hash=sha256:ef48e2707fb320c8f139424a596f5b69955a85b178f15af261bab871873bb987 \
     --hash=sha256:f152cbf5b88aaeb836127d920dd0f5e7edff5a66f10c079157306c4343d86c19 \
     --hash=sha256:fc0b4d8bfeabd25ea75e94632f5b6e047eef8adaed0c2161ada1e922e7f7cece
-    # via pytest-cov
+    # via
+    #   -r requirements/dev.in
+    #   pytest-cov
 distlib==0.3.8 \
     --hash=sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784 \
     --hash=sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64
@@ -189,15 +198,21 @@ filelock==3.14.0 \
 h11==0.14.0 \
     --hash=sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d \
     --hash=sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761
-    # via httpcore
+    # via
+    #   -c requirements/main.txt
+    #   httpcore
 httpcore==1.0.5 \
     --hash=sha256:34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61 \
     --hash=sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5
-    # via httpx
+    # via
+    #   -c requirements/main.txt
+    #   httpx
 httpx==0.27.0 \
     --hash=sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5 \
     --hash=sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5
-    # via respx
+    # via
+    #   -c requirements/main.txt
+    #   respx
 identify==2.5.36 \
     --hash=sha256:37d93f380f4de590500d9dba7db359d0d3da95ffe7f9de1753faa159e71e7dfa \
     --hash=sha256:e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d
@@ -206,6 +221,7 @@ idna==3.7 \
     --hash=sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc \
     --hash=sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0
     # via
+    #   -c requirements/main.txt
     #   anyio
     #   httpx
     #   requests
@@ -216,11 +232,15 @@ iniconfig==2.0.0 \
 jinja2==3.1.4 \
     --hash=sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369 \
     --hash=sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d
-    # via scriv
+    # via
+    #   -c requirements/main.txt
+    #   scriv
 markdown-it-py==3.0.0 \
     --hash=sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1 \
     --hash=sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb
-    # via scriv
+    # via
+    #   -c requirements/main.txt
+    #   scriv
 markupsafe==2.1.5 \
     --hash=sha256:00e046b6dd71aa03a41079792f8473dc494d564611a8f89bbbd7cb93295ebdcf \
     --hash=sha256:075202fa5b72c86ad32dc7d0b56024ebdbcf2048c0ba09f1cde31bfdd57bcfff \
@@ -282,11 +302,15 @@ markupsafe==2.1.5 \
     --hash=sha256:fa9db3f79de01457b03d4f01b34cf91bc0048eb2c3846ff26f66687c2f6d16ab \
     --hash=sha256:fce659a462a1be54d2ffcacea5e3ba2d74daa74f30f5f143fe0c58636e355fdd \
     --hash=sha256:ffee1f21e5ef0d712f9033568f8344d5da8cc2869dbd08d87c84656e6a2d2f68
-    # via jinja2
+    # via
+    #   -c requirements/main.txt
+    #   jinja2
 mdurl==0.1.2 \
     --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
     --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
-    # via markdown-it-py
+    # via
+    #   -c requirements/main.txt
+    #   markdown-it-py
 mypy==1.10.0 \
     --hash=sha256:075cbf81f3e134eadaf247de187bd604748171d6b79736fa9b6c9685b4083061 \
     --hash=sha256:12b6bfc1b1a66095ab413160a6e520e1dc076a28f3e22f7fb25ba3b000b4ef99 \
@@ -315,6 +339,7 @@ mypy==1.10.0 \
     --hash=sha256:f90cff89eea89273727d8783fef5d4a934be2fdca11b47def50cf5d311aff727 \
     --hash=sha256:fa7ef5244615a2523b56c034becde4e9e3f9b034854c93639adb667ec9ec2976 \
     --hash=sha256:fcfc70599efde5c67862a07a1aaf50e55bce629ace26bb19dc17cece5dd31ca4
+    # via -r requirements/dev.in
 mypy-extensions==1.0.0 \
     --hash=sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d \
     --hash=sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782
@@ -327,35 +352,41 @@ packaging==24.0 \
     --hash=sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5 \
     --hash=sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9
     # via
+    #   -c requirements/main.txt
     #   pytest
     #   pytest-sugar
-platformdirs==4.2.1 \
-    --hash=sha256:031cd18d4ec63ec53e82dceaac0417d218a6863f7745dfcc9efe7793b7039bdf \
-    --hash=sha256:17d5a1161b3fd67b390023cb2d3b026bbd40abde6fdb052dfbd3a29c3ba22ee1
+platformdirs==4.2.2 \
+    --hash=sha256:2d7a1657e36a80ea911db832a8a6ece5ee53d8de21edd5cc5879af6530b1bfee \
+    --hash=sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3
     # via virtualenv
 pluggy==1.5.0 \
     --hash=sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1 \
     --hash=sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669
     # via pytest
-pre-commit==3.7.0 \
-    --hash=sha256:5eae9e10c2b5ac51577c3452ec0a490455c45a0533f7960f993a0d01e59decab \
-    --hash=sha256:e209d61b8acdcf742404408531f0c37d49d2c734fd7cff2d6076083d191cb060
-pytest==8.2.0 \
-    --hash=sha256:1733f0620f6cda4095bbf0d9ff8022486e91892245bb9e7d5542c018f612f233 \
-    --hash=sha256:d507d4482197eac0ba2bae2e9babf0672eb333017bcedaa5fb1a3d42c1174b3f
+pre-commit==3.7.1 \
+    --hash=sha256:8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a \
+    --hash=sha256:fae36fd1d7ad7d6a5a1c0b0d5adb2ed1a3bda5a21bf6c3e5372073d7a11cd4c5
+    # via -r requirements/dev.in
+pytest==8.2.1 \
+    --hash=sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd \
+    --hash=sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1
     # via
+    #   -r requirements/dev.in
     #   pytest-asyncio
     #   pytest-cov
     #   pytest-sugar
-pytest-asyncio==0.23.6 \
-    --hash=sha256:68516fdd1018ac57b846c9846b954f0393b26f094764a28c955eabb0536a4e8a \
-    --hash=sha256:ffe523a89c1c222598c76856e76852b787504ddb72dd5d9b6617ffa8aa2cde5f
+pytest-asyncio==0.23.7 \
+    --hash=sha256:009b48127fbe44518a547bddd25611551b0e43ccdbf1e67d12479f569832c20b \
+    --hash=sha256:5f5c72948f4c49e7db4f29f2521d4031f1c27f86e57b046126654083d4770268
+    # via -r requirements/dev.in
 pytest-cov==5.0.0 \
     --hash=sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652 \
     --hash=sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857
+    # via -r requirements/dev.in
 pytest-sugar==1.0.0 \
     --hash=sha256:6422e83258f5b0c04ce7c632176c7732cab5fdb909cb39cca5c9139f81276c0a \
     --hash=sha256:70ebcd8fc5795dc457ff8b69d266a4e2e8a74ae0c3edc749381c64b5246c8dfd
+    # via -r requirements/dev.in
 pyyaml==6.0.1 \
     --hash=sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5 \
     --hash=sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc \
@@ -408,35 +439,42 @@ pyyaml==6.0.1 \
     --hash=sha256:fca0e3a251908a499833aa292323f32437106001d436eca0e6e7833256674585 \
     --hash=sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d \
     --hash=sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f
-    # via pre-commit
+    # via
+    #   -c requirements/main.txt
+    #   pre-commit
 requests==2.31.0 \
     --hash=sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f \
     --hash=sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1
-    # via scriv
+    # via
+    #   -c requirements/main.txt
+    #   scriv
 respx==0.21.1 \
     --hash=sha256:05f45de23f0c785862a2c92a3e173916e8ca88e4caad715dd5f68584d6053c20 \
     --hash=sha256:0bd7fe21bfaa52106caa1223ce61224cf30786985f17c63c5d71eff0307ee8af
-ruff==0.4.3 \
-    --hash=sha256:08a0d6a22918ab2552ace96adeaca308833873a4d7d1d587bb1d37bae8728eb3 \
-    --hash=sha256:0bfc9e955e6dc6359eb6f82ea150c4f4e82b660e5b58d9a20a0e42ec3bb6342b \
-    --hash=sha256:18b00e0bcccf0fc8d7186ed21e311dffd19761cb632241a6e4fe4477cc80ef6e \
-    --hash=sha256:25cacda2155778beb0d064e0ec5a3944dcca9c12715f7c4634fd9d93ac33fd30 \
-    --hash=sha256:262f5635e2c74d80b7507fbc2fac28fe0d4fef26373bbc62039526f7722bca1b \
-    --hash=sha256:29efff25bf9ee685c2c8390563a5b5c006a3fee5230d28ea39f4f75f9d0b6f2f \
-    --hash=sha256:510a67d232d2ebe983fddea324dbf9d69b71c4d2dfeb8a862f4a127536dd4cfb \
-    --hash=sha256:71ca5f8ccf1121b95a59649482470c5601c60a416bf189d553955b0338e34614 \
-    --hash=sha256:7363691198719c26459e08cc17c6a3dac6f592e9ea3d2fa772f4e561b5fe82a3 \
-    --hash=sha256:7a1c3a450bc6539ef00da6c819fb1b76b6b065dec585f91456e7c0d6a0bbc725 \
-    --hash=sha256:819fb06d535cc76dfddbfe8d3068ff602ddeb40e3eacbc90e0d1272bb8d97113 \
-    --hash=sha256:927b11c1e4d0727ce1a729eace61cee88a334623ec424c0b1c8fe3e5f9d3c865 \
-    --hash=sha256:b70800c290f14ae6fcbb41bbe201cf62dfca024d124a1f373e76371a007454ce \
-    --hash=sha256:dc9ff11cd9a092ee7680a56d21f302bdda14327772cd870d806610a3503d001f \
-    --hash=sha256:eba1f14df3c758dd7de5b55fbae7e1c8af238597961e5fb628f3de446c3c40c5 \
-    --hash=sha256:eeb039f8428fcb6725bb63cbae92ad67b0559e68b5d80f840f11914afd8ddf7f \
-    --hash=sha256:ff0a3ef2e3c4b6d133fbedcf9586abfbe38d076041f2dc18ffb2c7e0485d5a07
+    # via -r requirements/dev.in
+ruff==0.4.4 \
+    --hash=sha256:1aecced1269481ef2894cc495647392a34b0bf3e28ff53ed95a385b13aa45768 \
+    --hash=sha256:29d44ef5bb6a08e235c8249294fa8d431adc1426bfda99ed493119e6f9ea1bf6 \
+    --hash=sha256:39df0537b47d3b597293edbb95baf54ff5b49589eb7ff41926d8243caa995ea6 \
+    --hash=sha256:424e5b72597482543b684c11def82669cc6b395aa8cc69acc1858b5ef3e5daae \
+    --hash=sha256:4c8e2f1e8fc12d07ab521a9005d68a969e167b589cbcaee354cb61e9d9de9c15 \
+    --hash=sha256:60ed88b636a463214905c002fa3eaab19795679ed55529f91e488db3fe8976ab \
+    --hash=sha256:8e7e6ebc10ef16dcdc77fd5557ee60647512b400e4a60bdc4849468f076f6eef \
+    --hash=sha256:958b4ea5589706a81065e2a776237de2ecc3e763342e5cc8e02a4a4d8a5e6f95 \
+    --hash=sha256:9da73eb616b3241a307b837f32756dc20a0b07e2bcb694fec73699c93d04a69e \
+    --hash=sha256:b1867ee9bf3acc21778dcb293db504692eda5f7a11a6e6cc40890182a9f9e595 \
+    --hash=sha256:b5eb0a4bfd6400b7d07c09a7725e1a98c3b838be557fee229ac0f84d9aa49c36 \
+    --hash=sha256:b90fc5e170fc71c712cc4d9ab0e24ea505c6a9e4ebf346787a67e691dfb72e85 \
+    --hash=sha256:b9ddb2c494fb79fc208cd15ffe08f32b7682519e067413dbaf5f4b01a6087bcd \
+    --hash=sha256:c4efe62b5bbb24178c950732ddd40712b878a9b96b1d02b0ff0b08a090cbd891 \
+    --hash=sha256:c51c928a14f9f0a871082603e25a1588059b7e08a920f2f9fa7157b5bf08cfe9 \
+    --hash=sha256:cb53473849f011bca6e754f2cdf47cafc9c4f4ff4570003a0dad0b9b6890e876 \
+    --hash=sha256:f87ea42d5cdebdc6a69761a9d0bc83ae9b3b30d0ad78952005ba6568d6c022af
+    # via -r requirements/dev.in
 scriv==1.5.1 \
     --hash=sha256:30ae9ff8d144f8e0cf394c4e1d379542f1b3823767642955b54ec40dc00b32b6 \
     --hash=sha256:a3adc657733b4124fcb54527a5f3daab0d3c300de82d0fd2b9b297b243151b78
+    # via -r requirements/dev.in
 setuptools==69.5.1 \
     --hash=sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987 \
     --hash=sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32
@@ -445,6 +483,7 @@ sniffio==1.3.1 \
     --hash=sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2 \
     --hash=sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc
     # via
+    #   -c requirements/main.txt
     #   anyio
     #   asgi-lifespan
     #   httpx
@@ -455,20 +494,25 @@ termcolor==2.4.0 \
 types-pyyaml==6.0.12.20240311 \
     --hash=sha256:a9e0f0f88dc835739b0c1ca51ee90d04ca2a897a71af79de9aec5f38cb0a5342 \
     --hash=sha256:b845b06a1c7e54b8e5b4c683043de0d9caf205e7434b3edc678ff2411979b8f6
+    # via -r requirements/dev.in
 types-requests==2.31.0.20240406 \
     --hash=sha256:4428df33c5503945c74b3f42e82b181e86ec7b724620419a2966e2de604ce1a1 \
     --hash=sha256:6216cdac377c6b9a040ac1c0404f7284bd13199c0e1bb235f4324627e8898cf5
+    # via -r requirements/dev.in
 typing-extensions==4.11.0 \
     --hash=sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0 \
     --hash=sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a
-    # via mypy
+    # via
+    #   -c requirements/main.txt
+    #   mypy
 urllib3==2.2.1 \
     --hash=sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d \
     --hash=sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19
     # via
+    #   -c requirements/main.txt
     #   requests
     #   types-requests
-virtualenv==20.26.1 \
-    --hash=sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b \
-    --hash=sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75
+virtualenv==20.26.2 \
+    --hash=sha256:82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c \
+    --hash=sha256:a624db5e94f01ad993d476b9ee5346fdf7b9de43ccaee0e0197012dc838a0e9b
     # via pre-commit