chore(main): release 3.0.0

.github/workflows/cd.yml

@@ -149,4 +149,4 @@ jobs:
           push: true
           cache-from: type=gha
           cache-to: type=gha,mode=max
-          no-cache: true # This line enables building without using any cache
+          no-cache: true # This line enables building without using any cache

CHANGELOG.md

@@ -1,5 +1,107 @@
 # Changelog
 
+## [3.0.0](https://github.com/CIRADA-Tools/science-containers/compare/v2.0.2...v3.0.0) (2026-05-26)
+
+
+### ⚠ BREAKING CHANGES
+
+* update from prefect2 to prefect3
+* Version 1, first production version
+
+### Features
+
+* add astroquery ([c52d88e](https://github.com/CIRADA-Tools/science-containers/commit/c52d88ee7338bbfe7d606513d72b4bc5c0e029cc))
+* add bagpipes ([7b53ee4](https://github.com/CIRADA-Tools/science-containers/commit/7b53ee46fbb54e1ced34500aee784a6df9c8c379))
+* add cartopy and psycopg2-binary for status page ([cb0ae8a](https://github.com/CIRADA-Tools/science-containers/commit/cb0ae8a039f16602ba2131c8fe0e38872e502d70))
+* Add java to notebook version ([fc2404c](https://github.com/CIRADA-Tools/science-containers/commit/fc2404c0fa83b0a3dd09c93af690c2ea879d80fb))
+* Add java to notebook version try2 ([526fd55](https://github.com/CIRADA-Tools/science-containers/commit/526fd5519cfc7e8900625b8198044c27176a9a0e))
+* Add java to notebook version try3 ([0b4c80c](https://github.com/CIRADA-Tools/science-containers/commit/0b4c80c4dfaeeed6413882f0c89a5670acd2511b))
+* Add java to notebook version try4 ([e80cbfb](https://github.com/CIRADA-Tools/science-containers/commit/e80cbfb6a5f4b7bd5d7fcad0aeebfaee54b71fd3))
+* add MPI ([e8f1924](https://github.com/CIRADA-Tools/science-containers/commit/e8f19249b6708cf856fbb76e6a4a0bc930d91fa2))
+* Add pyfftw ([2585c42](https://github.com/CIRADA-Tools/science-containers/commit/2585c42f891f3040b44ef40c36f0d57c4580d7db))
+* add python-dotenv for POSSUMutils ([ff6e81a](https://github.com/CIRADA-Tools/science-containers/commit/ff6e81a78527882614b3990d6dcc93d58f7e103e))
+* add singularity, apptainer and screen ([6c46c84](https://github.com/CIRADA-Tools/science-containers/commit/6c46c84f8044fe766ac79f9de8585187e6688486))
+* add utilities for possum2caom2 ([a89e5ad](https://github.com/CIRADA-Tools/science-containers/commit/a89e5ad444100136c276893c05d3a0e2cb866536))
+* **base Image:** debugged micromamba installation process ([4a6b0ac](https://github.com/CIRADA-Tools/science-containers/commit/4a6b0acc470da7ffc265459d4de443464ecbb607))
+* **base:** add beautifulsoup module ([fb425ee](https://github.com/CIRADA-Tools/science-containers/commit/fb425ee41c9233b752e2f4e38e157505078a52a1))
+* **base:** Add no cache to continuous development whenever possum2caom2 needs to be updated ([c097797](https://github.com/CIRADA-Tools/science-containers/commit/c0977976746d87a71c2cd8c0d3c2105ffb259562))
+* **base:** add rclone ([3b82ecf](https://github.com/CIRADA-Tools/science-containers/commit/3b82ecf45035492727f79c5d2f147e50f06d4a6a))
+* **base:** add sssd to prefect container ([3894c4f](https://github.com/CIRADA-Tools/science-containers/commit/3894c4f4eaf3995204825705f7b9a75f2762ea27))
+* **base:** add tk to prefect container ([38c51c0](https://github.com/CIRADA-Tools/science-containers/commit/38c51c058044b482fb1c0f4632d979a51ac74d34))
+* **base:** implement prefect in separate container ([73c1005](https://github.com/CIRADA-Tools/science-containers/commit/73c1005186e62c47f38ebdd60df6d9eea7d6ad02))
+* **base:** remove possum_headless from CD and add POSSUM2CAOM2 software ([cdcb63b](https://github.com/CIRADA-Tools/science-containers/commit/cdcb63bf219310b441cca51107482bc92669bd67))
+* **base:** try install prefect in headless docker container ([d25b7c5](https://github.com/CIRADA-Tools/science-containers/commit/d25b7c5c811adf6d69485d9c35d99bddc9a77509))
+* **base:** Unify Dockerfile for notebook and headless. Add prefect to notebook, no jupyter in headless ([2c3c1d6](https://github.com/CIRADA-Tools/science-containers/commit/2c3c1d67b61b333adcf23c3aecb586087d38b4ef))
+* **build:** add quotes around python versions ([a64ef9b](https://github.com/CIRADA-Tools/science-containers/commit/a64ef9be5945c9cba1e0634317aa6503d2e06392))
+* **ci:** added pre-commit ci action ([2cc8b3d](https://github.com/CIRADA-Tools/science-containers/commit/2cc8b3d92aeca39e3605a38d2fe3e90fbe36c347))
+* **core:** also push notebook images ([214cdfc](https://github.com/CIRADA-Tools/science-containers/commit/214cdfc71ad4959df3292877e83d2c49c8a0719a))
+* **core:** install yappi and psrecord ([be51367](https://github.com/CIRADA-Tools/science-containers/commit/be51367c6cc1ca50bbb559cd8a5c0428a5f09bdb))
+* **core:** remove POSSUM pipeline code copy ([92c10f4](https://github.com/CIRADA-Tools/science-containers/commit/92c10f4e22557a46591e059d40332658fa4a03fe))
+* **docs:** added mkdocs ([8505ae8](https://github.com/CIRADA-Tools/science-containers/commit/8505ae80f38eefda829eba3b1de201326f80d095))
+* downgrade astroquery so I can login headlessly ([f069f82](https://github.com/CIRADA-Tools/science-containers/commit/f069f8255896e7951f5862ad162f5831e6169481))
+* force update caom2repo to 1.6.3 ([8a11a7b](https://github.com/CIRADA-Tools/science-containers/commit/8a11a7b866bcd6d5ab11913f2913b8f75ad3f614))
+* **Github-Actions:** added a new deployment step with matrix capabilties ([1d2b711](https://github.com/CIRADA-Tools/science-containers/commit/1d2b71185d9e757a7fc7588c2e375704514d1522))
+* **Github-Actions:** added deloyment action for base container ([32df4a2](https://github.com/CIRADA-Tools/science-containers/commit/32df4a2cb4183ba57996524f2735f45e5c9d9b20))
+* install FITSverify into notebook ([da6a8c3](https://github.com/CIRADA-Tools/science-containers/commit/da6a8c3f5da44a61fd6831a02f4e9777d7bb1d32))
+* install pyregion ([2d76a41](https://github.com/CIRADA-Tools/science-containers/commit/2d76a4123bf404f112267d8c2fe9bcd33cdda74e))
+* remove pyfftw and install cadctap pyvo and vos for interacting with youCAT ([76a4e2e](https://github.com/CIRADA-Tools/science-containers/commit/76a4e2e42a1af4fcdeb5ee3efb3a508ed0118091))
+* **setup:** added python setup config ([e740204](https://github.com/CIRADA-Tools/science-containers/commit/e740204bef364144902201fbeb8ed6431536c7e3))
+* update from prefect2 to prefect3 ([a1eb503](https://github.com/CIRADA-Tools/science-containers/commit/a1eb503e2e9c885f05ac128870b67cbe1d740dd1))
+* Version 1, first production version ([47bc23f](https://github.com/CIRADA-Tools/science-containers/commit/47bc23f1cc9925d0387a87911f9425233721c1d2))
+
+
+### Bug Fixes
+
+* add bagpipes back in to resolve dependencies ([49f4fcc](https://github.com/CIRADA-Tools/science-containers/commit/49f4fcc66834023798ad4cbf299a3aa2dc4ee6b5))
+* Add java to docker try10 ([fa46979](https://github.com/CIRADA-Tools/science-containers/commit/fa469797a997fc8774f251078fd882ffb28bbcd3))
+* Add java to docker try11 (just notebook) ([7763496](https://github.com/CIRADA-Tools/science-containers/commit/7763496801d42b66a41d04bce759ca6905da99e5))
+* Add java to docker try12 (jre instead of jdk) ([cfbd323](https://github.com/CIRADA-Tools/science-containers/commit/cfbd323713a164c48aefe21fd9a34a87ad88e7ae))
+* Add java to docker try6 ([748bbe4](https://github.com/CIRADA-Tools/science-containers/commit/748bbe4fb9291a41f8fe49ce5bcd59286892e1cd))
+* Add java to docker try7 ([29b3cdb](https://github.com/CIRADA-Tools/science-containers/commit/29b3cdb42d1424edc9a819bfdb52a9439c51aaba))
+* Add java to docker try8 ([6b0cf4c](https://github.com/CIRADA-Tools/science-containers/commit/6b0cf4cbb72e1e786d7673d1f995b59b1438e48c))
+* Add java to docker try9 ([8f1b0a2](https://github.com/CIRADA-Tools/science-containers/commit/8f1b0a2745d68e455cb65b33121d4748fd855701))
+* Add java to notebook version try5 ([dae0cd2](https://github.com/CIRADA-Tools/science-containers/commit/dae0cd23451c7cbcb7840919b3334f33aac68200))
+* **base:** Also add possum2caom2 to notebook ([c73b877](https://github.com/CIRADA-Tools/science-containers/commit/c73b87777d1b18ef0f2d5ebf32604d233a65de32))
+* **base:** CANFAR requires sssd ([ae21bf6](https://github.com/CIRADA-Tools/science-containers/commit/ae21bf6f982f9efb0ad34868f4571f358ca99365))
+* **base:** move to py3.12 ([5e294cb](https://github.com/CIRADA-Tools/science-containers/commit/5e294cb2d4828ddb5dd96e4e5f34758adc65090c))
+* **base:** Moving to py3.12 ([7d5dd5e](https://github.com/CIRADA-Tools/science-containers/commit/7d5dd5e782944585d86589a9a5419fafffade51f))
+* **base:** rclone requires unzip ([4f8e87c](https://github.com/CIRADA-Tools/science-containers/commit/4f8e87c6e58cdc971cd6f0be760a6ccacdd2c8b3))
+* **build:** fixed ref issue in docker build ([d971218](https://github.com/CIRADA-Tools/science-containers/commit/d971218673fd62ff139db6fd7fc2fa1aeea138f8))
+* **CI/CD:** fixed issues with docs build ([1661518](https://github.com/CIRADA-Tools/science-containers/commit/1661518052492836200733459ed2aa4230024103))
+* **core:** add gprof2dot ([db32043](https://github.com/CIRADA-Tools/science-containers/commit/db320436f9fa89ef0a8c45fb7cf0dd9ec831809e))
+* **docs:** fixed the spelling of ubuntu ([ff272b3](https://github.com/CIRADA-Tools/science-containers/commit/ff272b3d0033a970d7d8dce8b4d3417732953edc))
+* downgrade astroquery so I can login headlessly ([246ac72](https://github.com/CIRADA-Tools/science-containers/commit/246ac7231217eb6ee33ad2f4540f6c2709cd84f9))
+* fix pymultinest installation ([0babf21](https://github.com/CIRADA-Tools/science-containers/commit/0babf2154974903b60c4c88fe42ba0059e44f527))
+* force update containers to get new possum2caom2 version ([04fd6e0](https://github.com/CIRADA-Tools/science-containers/commit/04fd6e00ebaeb6651ffc9da8058bd13cb8e9d3fa))
+* force update possum2caom ([6649940](https://github.com/CIRADA-Tools/science-containers/commit/6649940c216a6e308f1516171e0fbbeff3ebf456))
+* Force update to latest possum2caom2 ([1be123d](https://github.com/CIRADA-Tools/science-containers/commit/1be123d16a110df459e20d8be6ec96eb5638c19d))
+* **Github-Actions:** fixed github actions syntax ([beafcc6](https://github.com/CIRADA-Tools/science-containers/commit/beafcc65d8103fe09375a6206845b80549319935))
+* **Github-Actions:** working on deployment ([d19c775](https://github.com/CIRADA-Tools/science-containers/commit/d19c775de05eeb51931e68f72930a9b89c441303))
+* **Github-Actions:** working on deployment chain ([c14f04d](https://github.com/CIRADA-Tools/science-containers/commit/c14f04dbf0a46db26821f2aa9134c9b438665ae8))
+* **possum_prefect:** rebuild to pick up healpy-based possum2caom2 (fixes 0923 vs 0922 tile names) ([9ceb2d9](https://github.com/CIRADA-Tools/science-containers/commit/9ceb2d90c4a8ebdf5bd7153d903bf32a4e8f23ee))
+* remove pyfftw as it doesnt work with py312 ([959109a](https://github.com/CIRADA-Tools/science-containers/commit/959109a7dac278c833d2f89c50c6657b5a699357))
+* remove singularity ([0c7be0c](https://github.com/CIRADA-Tools/science-containers/commit/0c7be0ce089083cc8f044a19d5699aff69ada41f))
+* should have been psycopg2-binary' ([285a038](https://github.com/CIRADA-Tools/science-containers/commit/285a038997f054229519bc62154187cbec1fab37))
+* standardise on prefect 3.4.25 for now ([9850716](https://github.com/CIRADA-Tools/science-containers/commit/9850716881eac482646704e37de66db14a701df0))
+* this should finally install apptainer/singularity ([c9c8f99](https://github.com/CIRADA-Tools/science-containers/commit/c9c8f992129e18b18735871e7514bd302e9b3865))
+* try fix with dev version ([906c5fe](https://github.com/CIRADA-Tools/science-containers/commit/906c5fe2372deb0a3b22bd338222e9c2cd439e17))
+* try fix with mkdir ([557cfda](https://github.com/CIRADA-Tools/science-containers/commit/557cfdaff70a2065a4e500e59bbfc26573732bd7))
+* update dockerfile to address bug ([5e2b4d9](https://github.com/CIRADA-Tools/science-containers/commit/5e2b4d92e62d14ceb0295a4bd8e7d710294cb06a))
+* update readme ([952c6ac](https://github.com/CIRADA-Tools/science-containers/commit/952c6ac9cbc81ea2a3d1dc3d0ccffea574b6b076))
+* Update README (and force building new version of possum2caom2) ([b275161](https://github.com/CIRADA-Tools/science-containers/commit/b2751614e650ea9557142e487e15a974fb7a7047))
+* update README and force new build to update possum2caom2 ([6955d1f](https://github.com/CIRADA-Tools/science-containers/commit/6955d1fadca24e9715ff3985e8625511a9c25571))
+* update README and force new build to update possum2caom2 v0.1.4 ([80fd30c](https://github.com/CIRADA-Tools/science-containers/commit/80fd30cae06fcf7cb1646f5b7ebc1471c7f59f9f))
+* Working version of fitsverify in both containers ([6e5d348](https://github.com/CIRADA-Tools/science-containers/commit/6e5d34832dc636b11c5d2c0853e9707e4eb85749))
+
+
+### Documentation
+
+* **docs:** initial port from science-containers ([af7abaf](https://github.com/CIRADA-Tools/science-containers/commit/af7abaf9276c51b2b6e6a748f0ffc9a179202932))
+* **docs:** root README.md ([68ea7d3](https://github.com/CIRADA-Tools/science-containers/commit/68ea7d3a20e80dac9ffe0c689b7e4e11a2083dff))
+* **docs:** root README.md ([c31227c](https://github.com/CIRADA-Tools/science-containers/commit/c31227c998cafbd7f4fe1af103989ccc3c1abe20))
+* **rework:** index rework ([0072015](https://github.com/CIRADA-Tools/science-containers/commit/00720150466de4de4d2097a405f839e0ff48d764))
+* **rework:** rework ([5bc217c](https://github.com/CIRADA-Tools/science-containers/commit/5bc217cc11b4ab72b156d8f96f8d35995b4a8d2b))
+
 ## [2.0.2](https://github.com/ErikOsinga/science-containers/compare/v2.0.1...v2.0.2) (2026-02-06)
 
 

README.md

@@ -2,7 +2,7 @@
 
 This repository hosts Docker container configurations for the VLASS* and POSSUM pipelines, optimized for deployment on the CANFAR Science Platform but more broadly employable as well. These containers are designed to facilitate scientific computing tasks in a reproducible and scalable manner. The repository is based on the original repository found [here](https://github.com/opencadc/science-containers/).
 
-For POSSUM there are currently two Dockerfiles, which have identical software, except that the 'notebook' version installs jupyterlab, while the 'headless' version does not. 
+For POSSUM there are currently two Dockerfiles, which have identical software, except that the 'notebook' version installs jupyterlab, while the 'headless' version does not.
 
 
 ## Usage
@@ -58,12 +58,10 @@ Version 1.14 and up have a downgraded version of astroquery to allow headless lo
 
 Version 1.13 and above will contain singularity/apptainer and screen
 
-Version 1.7.5 Contains possum2caom2 as of 2024-08-20, which has the ingest set-up for the 3D pipeline. 
+Version 1.7.5 Contains possum2caom2 as of 2024-08-20, which has the ingest set-up for the 3D pipeline.
 
-Version 1.7 now contains fitsverify, part of libcfitsio-bin. Version 1.7.4 should contain a new version of possum2caom2 (caom2 to version 2.6.2 and caom2utils to version 1.7.3,  0.1.6 of possum2caom2) which (hopefully) fixes ingesting 3D FDFs and RMSF into CADC. 
+Version 1.7 now contains fitsverify, part of libcfitsio-bin. Version 1.7.4 should contain a new version of possum2caom2 (caom2 to version 2.6.2 and caom2utils to version 1.7.3,  0.1.6 of possum2caom2) which (hopefully) fixes ingesting 3D FDFs and RMSF into CADC.
 
-Version 1.6 (2024-07-16) now contains java (jre) and cadctap pyvo and vos as well. Note that pyfftw does not work with py3.12 as of 2024-07-23 but there is a separate container available on CANFAR which runs py3.11. Additionally there is also a container available that contains a 2022 version of WSclean (both not maintained on this GitHub page though). 
+Version 1.6 (2024-07-16) now contains java (jre) and cadctap pyvo and vos as well. Note that pyfftw does not work with py3.12 as of 2024-07-23 but there is a separate container available on CANFAR which runs py3.11. Additionally there is also a container available that contains a 2022 version of WSclean (both not maintained on this GitHub page though).
 
 Version 1.0 (2024-05-16) is now here! The POSSUM polarimetry processing is now in full-swing and working (so far), so it is time for version 1.0.
-
-

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "science-containers"
-version = "2.0.2"
+version = "3.0.0"
 description = "Science Containers for CANFAR"
 authors = ["CANFAR <support@canfar.net>"]
 license = "GNU Affero GPL v3.0"

science-containers/Dockerfiles/base/Dockerfile

@@ -23,7 +23,7 @@ RUN apt-get update --yes --quiet --fix-missing \
         tcsh \
     && apt-get clean --yes \
     && apt-get autoremove --purge --quiet --yes \
-    && rm -rf /var/lib/apt/lists/* /var/tmp/* 
+    && rm -rf /var/lib/apt/lists/* /var/tmp/*
 
 ADD nsswitch.conf /etc/
 

science-containers/Dockerfiles/possum_notebook/Dockerfile

@@ -1,5 +1,5 @@
 FROM prefecthq/prefect:3.4.25-python3.12-kubernetes
-# see available versions at 
+# see available versions at
 # https://hub.docker.com/r/prefecthq/prefect/
 
 
@@ -36,9 +36,9 @@ RUN apt-get update --yes --quiet --fix-missing \
         screen \
     && apt-get clean --yes \
     && apt-get autoremove --purge --quiet --yes \
-    && rm -rf /var/lib/apt/lists/* /var/tmp/* 
+    && rm -rf /var/lib/apt/lists/* /var/tmp/*
 
-# install rclone 
+# install rclone
 RUN sudo -v ; curl https://rclone.org/install.sh | sudo bash
 
 ADD nsswitch.conf /etc/
@@ -97,7 +97,7 @@ RUN pip install numpy \
     prefect \
     pyregion \
     tqdm
-    
+
 # Install other python packages with pip
 RUN pip install RM-Tools \
     RMTable \
@@ -176,5 +176,5 @@ RUN git clone https://github.com/${OPENCADC_REPO}/caom2tools.git && \
 RUN pip install git+https://github.com/${OPENCADC_REPO}/caom2pipe@${OPENCADC_BRANCH}#egg=caom2pipe
 RUN pip install git+https://github.com/${OPENCADC_REPO}/possum2caom2@${OPENCADC_BRANCH}#egg=possum2caom2
 
-# Get jupyter in the headless version 
+# Get jupyter in the headless version
 RUN pip install jupyterlab

science-containers/Dockerfiles/possum_prefect/Dockerfile

@@ -1,5 +1,5 @@
 FROM prefecthq/prefect:3.4.25-python3.12-kubernetes
-# see available versions at 
+# see available versions at
 # https://hub.docker.com/r/prefecthq/prefect/
 
 LABEL maintainer="Erik Osinga <erik.osinga@utoronto.ca>"
@@ -32,9 +32,9 @@ RUN apt-get update --yes --quiet --fix-missing \
         default-jre \
     && apt-get clean --yes \
     && apt-get autoremove --purge --quiet --yes \
-    && rm -rf /var/lib/apt/lists/* /var/tmp/* 
+    && rm -rf /var/lib/apt/lists/* /var/tmp/*
 
-# install rclone 
+# install rclone
 RUN sudo -v ; curl https://rclone.org/install.sh | sudo bash
 
 ADD nsswitch.conf /etc/
@@ -49,7 +49,7 @@ RUN pip install numpy \
     prefect \
     pyregion \
     tqdm
-    
+
 # Install other python packages with pip
 RUN pip install RM-Tools \
     RMTable \
@@ -126,5 +126,5 @@ RUN pip install git+https://github.com/${OPENCADC_REPO}/caom2pipe@${OPENCADC_BRA
 # 2026-05-26: rebuild to pick up healpy-based possum2caom2 (fixes 0923 vs 0922 tile coordinate names)
 RUN pip install git+https://github.com/${OPENCADC_REPO}/possum2caom2@${OPENCADC_BRANCH}#egg=possum2caom2
 
-# dont get jupyter in the headless version 
+# dont get jupyter in the headless version
 ### RUN pip install jupyterlab