From 6be7c590e2a97332473fccb5c7fb8bd7db7b33b5 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 4 Sep 2025 16:38:30 -0400 Subject: [PATCH 01/19] Prep for 2025-3.0 envs --- configs/config-py310.yml | 4 ++-- configs/config-py311.yml | 4 ++-- configs/config-py312.yml | 4 ++-- envs/env-py310.yml | 2 +- envs/env-py311.yml | 2 +- envs/env-py312.yml | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/configs/config-py310.yml b/configs/config-py310.yml index a2ae0e3..a0f7411 100644 --- a/configs/config-py310.yml +++ b/configs/config-py310.yml @@ -1,5 +1,5 @@ docker_image: "quay.io/condaforge/linux-anvil-cos7-x86_64:latest" -env_name: "2025-2.2-py310-tiled" +env_name: "2025-3.0-py310-tiled" conda_env_file: "env-py310.yml" conda_binary: "mamba" python_version: "3.10" @@ -19,7 +19,7 @@ zenodo_metadata: title: "NSLS-II collection conda environment" upload_type: "software" description: "NSLS-II collection conda environment" - version: 2025-2.2-tiled + version: 2025-3.0-tiled creators: - name: Rakitin, Max affiliation: "Brookhaven National Laboratory" diff --git a/configs/config-py311.yml b/configs/config-py311.yml index 8232111..64095f5 100644 --- a/configs/config-py311.yml +++ b/configs/config-py311.yml @@ -1,5 +1,5 @@ docker_image: "quay.io/condaforge/linux-anvil-cos7-x86_64:latest" -env_name: "2025-2.2-py311-tiled" +env_name: "2025-3.0-py311-tiled" conda_env_file: "env-py311.yml" conda_binary: "mamba" python_version: "3.11" @@ -19,7 +19,7 @@ zenodo_metadata: title: "NSLS-II collection conda environment" upload_type: "software" description: "NSLS-II collection conda environment" - version: 2025-2.2-tiled + version: 2025-3.0-tiled creators: - name: Rakitin, Max affiliation: "Brookhaven National Laboratory" diff --git a/configs/config-py312.yml b/configs/config-py312.yml index e14151d..ff0f62b 100644 --- a/configs/config-py312.yml +++ b/configs/config-py312.yml @@ -1,5 +1,5 @@ docker_image: "quay.io/condaforge/linux-anvil-cos7-x86_64:latest" -env_name: "2025-2.2-py312-tiled" +env_name: "2025-3.0-py312-tiled" conda_env_file: "env-py312.yml" conda_binary: "mamba" python_version: "3.12" @@ -19,7 +19,7 @@ zenodo_metadata: title: "NSLS-II collection conda environment" upload_type: "software" description: "NSLS-II collection conda environment" - version: 2025-2.2-tiled + version: 2025-3.0-tiled creators: - name: Rakitin, Max affiliation: "Brookhaven National Laboratory" diff --git a/envs/env-py310.yml b/envs/env-py310.yml index df35ff1..80816f4 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -1,4 +1,4 @@ -name: 2025-2.2-py310-tiled +name: 2025-3.0-py310-tiled channels: - conda-forge dependencies: diff --git a/envs/env-py311.yml b/envs/env-py311.yml index 50ac6cb..d14e097 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -1,4 +1,4 @@ -name: 2025-2.2-py311-tiled +name: 2025-3.0-py311-tiled channels: - conda-forge dependencies: diff --git a/envs/env-py312.yml b/envs/env-py312.yml index fef1eda..e6f3380 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -1,4 +1,4 @@ -name: 2025-2.2-py312-tiled +name: 2025-3.0-py312-tiled channels: - conda-forge dependencies: From b5bb3b88c2385c2f9e8cab7710024fadfeef5368 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 4 Sep 2025 16:44:44 -0400 Subject: [PATCH 02/19] CI: use micromamba action v1.11.0 --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index ca3539c..753889d 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -113,7 +113,7 @@ jobs: sudo rm -f /usr/share/miniconda/.condarc - name: Setup umamba - uses: mamba-org/setup-micromamba@b09ef9b599704322748535812ca03efb2625677b # v2 + uses: mamba-org/setup-micromamba@4b9113af4fba0e9e1124b252dd6497a419e7396d # v1.11.0 with: environment-file: envs/env-py${{ env.PYTHONVER }}.yml log-level: info From 69c01a8b180a6a0206720e75dbb6a95ff538721c Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 4 Sep 2025 16:54:33 -0400 Subject: [PATCH 03/19] CI: use the latest version of setup-micromamba action (v2.0.6) --- .github/workflows/package.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index 753889d..ffab2b0 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -113,10 +113,10 @@ jobs: sudo rm -f /usr/share/miniconda/.condarc - name: Setup umamba - uses: mamba-org/setup-micromamba@4b9113af4fba0e9e1124b252dd6497a419e7396d # v1.11.0 + uses: mamba-org/setup-micromamba@7f29b8b80078b1b601dfa018b0f7425c587c63bb # v2.0.6 with: environment-file: envs/env-py${{ env.PYTHONVER }}.yml - log-level: info + log-level: debug env: CONDA_OVERRIDE_GLIBC: "2.28" From 80fa7ff937b1bd1a6f7e09beaf16832e334a0231 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Fri, 5 Sep 2025 10:28:28 -0400 Subject: [PATCH 04/19] Update minimum requirements --- envs/env-py310.yml | 16 +++++++++------- envs/env-py311.yml | 16 +++++++++------- envs/env-py312.yml | 16 +++++++++------- 3 files changed, 27 insertions(+), 21 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 80816f4..b7e9483 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -18,18 +18,19 @@ dependencies: - awkward - black - blosc-hdf5-plugin - - bluesky >=1.14.2 + - bluesky >=1.14.4 - bluesky-adaptive >=0.3.1 - bluesky-kafka >=0.10.0 - bluesky-live >=0.0.8 - bluesky-queueserver >=0.0.19 - bluesky-queueserver-api >=0.0.10 - - bluesky-tiled-plugins >=2.0.0b64 + - bluesky-tiled-plugins >=2.0.0b68 - bluesky-widgets >=0.0.15 - bokeh - boto3 - bottleneck # - broh5 + - cditools >=0.1.0 - chxtools - cmasher - conda-pack @@ -43,7 +44,7 @@ dependencies: - dask-jobqueue - dask-ml - dask-xgboost - - databroker >=2.0.0b64 + - databroker >=2.0.0b68 - datview - dictdiffer - diffpy.pdffit2 @@ -108,14 +109,14 @@ dependencies: - nexpy >=1.0.7 - nodejs - nsls2-detector-handlers >=0.0.3 - - nslsii >=0.11.1 + - nslsii >=0.11.4 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 - oct2py - opencv - openmpi >=4.1.4 - - ophyd >=1.10.5 + - ophyd >=1.11.0 # pandas and deps - pandas - openpyxl # used by pandas .to_excel() @@ -165,6 +166,7 @@ dependencies: - redis-py - reportlab - requests + - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn @@ -184,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b29 + - tiled >=0.1.0b39 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 @@ -214,7 +216,7 @@ dependencies: # - gladier-tools - h5json - mimesis - - ophyd-async[ca,pva] >=0.10.0a2 + - ophyd-async[ca,pva] >=0.13.1 - ortools - pyhyperscattering[bluesky,ui] >=0.2.9 - refuse diff --git a/envs/env-py311.yml b/envs/env-py311.yml index d14e097..1999373 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -18,18 +18,19 @@ dependencies: - awkward - black - blosc-hdf5-plugin - - bluesky >=1.14.2 + - bluesky >=1.14.4 - bluesky-adaptive >=0.3.1 - bluesky-kafka >=0.10.0 - bluesky-live >=0.0.8 - bluesky-queueserver >=0.0.19 - bluesky-queueserver-api >=0.0.10 - - bluesky-tiled-plugins >=2.0.0b64 + - bluesky-tiled-plugins >=2.0.0b68 - bluesky-widgets >=0.0.15 - bokeh - boto3 - bottleneck # - broh5 + - cditools >=0.1.0 - chxtools - cmasher - conda-pack @@ -43,7 +44,7 @@ dependencies: - dask-jobqueue - dask-ml - dask-xgboost - - databroker >=2.0.0b64 + - databroker >=2.0.0b68 - datview - dictdiffer - diffpy.pdffit2 @@ -108,14 +109,14 @@ dependencies: - nexpy >=1.0.7 - nodejs - nsls2-detector-handlers >=0.0.3 - - nslsii >=0.11.1 + - nslsii >=0.11.4 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 - oct2py - opencv - openmpi >=4.1.4 - - ophyd >=1.10.5 + - ophyd >=1.11.0 # pandas and deps - pandas - openpyxl # used by pandas .to_excel() @@ -165,6 +166,7 @@ dependencies: - redis-py - reportlab - requests + - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn @@ -184,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b29 + - tiled >=0.1.0b39 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 @@ -214,7 +216,7 @@ dependencies: # - gladier-tools - h5json - mimesis - - ophyd-async[ca,pva] >=0.10.0a2 + - ophyd-async[ca,pva] >=0.13.1 - ortools - pyhyperscattering[bluesky,ui] >=0.2.9 - refuse diff --git a/envs/env-py312.yml b/envs/env-py312.yml index e6f3380..c7c7530 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -18,18 +18,19 @@ dependencies: - awkward - black - blosc-hdf5-plugin - - bluesky >=1.14.2 + - bluesky >=1.14.4 - bluesky-adaptive >=0.3.1 - bluesky-kafka >=0.10.0 - bluesky-live >=0.0.8 - bluesky-queueserver >=0.0.19 - bluesky-queueserver-api >=0.0.10 - - bluesky-tiled-plugins >=2.0.0b64 + - bluesky-tiled-plugins >=2.0.0b68 - bluesky-widgets >=0.0.15 - bokeh - boto3 - bottleneck # - broh5 + - cditools >=0.1.0 - chxtools - cmasher - conda-pack @@ -43,7 +44,7 @@ dependencies: - dask-jobqueue - dask-ml - dask-xgboost - - databroker >=2.0.0b64 + - databroker >=2.0.0b68 - datview - dictdiffer - diffpy.pdffit2 @@ -108,14 +109,14 @@ dependencies: - nexpy >=1.0.7 - nodejs - nsls2-detector-handlers >=0.0.3 - - nslsii >=0.11.1 + - nslsii >=0.11.4 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 - oct2py - opencv - openmpi >=4.1.4 - - ophyd >=1.10.5 + - ophyd >=1.11.0 # pandas and deps - pandas - openpyxl # used by pandas .to_excel() @@ -165,6 +166,7 @@ dependencies: - redis-py - reportlab - requests + - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn @@ -184,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b29 + - tiled >=0.1.0b39 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 @@ -214,7 +216,7 @@ dependencies: # - gladier-tools - h5json - mimesis - - ophyd-async[ca,pva] >=0.10.0a2 + - ophyd-async[ca,pva] >=0.13.1 - ortools - pyhyperscattering[bluesky,ui] >=0.2.9 - refuse From 2abaae69f8ed90b5ee6e4ebc9f10673efd543ed7 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Fri, 5 Sep 2025 11:55:42 -0400 Subject: [PATCH 05/19] Export YAML --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index ffab2b0..1b2fd2a 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -150,7 +150,7 @@ jobs: - name: Export of the env .yml file run: | - conda env export -f ${ARTIFACTS_DIR}/${CONDA_PACK_ENV_NAME}.yml + conda env export -f ${ARTIFACTS_DIR}/${CONDA_PACK_ENV_NAME}.yml --format=yaml cat ${ARTIFACTS_DIR}/${CONDA_PACK_ENV_NAME}.yml # https://github.com/actions/upload-artifact From fd139a21e22cf63700195a595e7298c03c02ec6a Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Sun, 7 Sep 2025 11:59:21 -0400 Subject: [PATCH 06/19] Comment out julia packages --- envs/env-py310.yml | 4 ++-- envs/env-py311.yml | 4 ++-- envs/env-py312.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index b7e9483..55d1dbf 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -87,8 +87,8 @@ dependencies: - ispyb - isstools - jedi - - julia - - juliaup + # - julia + # - juliaup - jupyter - jupyterlab - larixite diff --git a/envs/env-py311.yml b/envs/env-py311.yml index 1999373..8136ba5 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -87,8 +87,8 @@ dependencies: - ispyb - isstools - jedi - - julia - - juliaup + # - julia + # - juliaup - jupyter - jupyterlab - larixite diff --git a/envs/env-py312.yml b/envs/env-py312.yml index c7c7530..8d2a987 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -87,8 +87,8 @@ dependencies: - ispyb - isstools - jedi - - julia - - juliaup + # - julia + # - juliaup - jupyter - jupyterlab - larixite From 145590495c1b663148ffca88cb599f64deec9336 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Sun, 7 Sep 2025 12:09:49 -0400 Subject: [PATCH 07/19] Comment out `rich` due to a conflict --- envs/env-py310.yml | 2 +- envs/env-py311.yml | 2 +- envs/env-py312.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 55d1dbf..fd394b0 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - - rich >=14.1.0 + # - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn diff --git a/envs/env-py311.yml b/envs/env-py311.yml index 8136ba5..dfe86a6 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - - rich >=14.1.0 + # - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 8d2a987..0901ec8 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - - rich >=14.1.0 + # - rich >=14.1.0 # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn From 40b74f570fa1876b6bb7880f29ef0e858ca76d39 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Mon, 8 Sep 2025 10:05:58 -0400 Subject: [PATCH 08/19] No py310; add rich without a pin --- .github/workflows/package.yml | 2 +- envs/env-py310.yml | 2 +- envs/env-py311.yml | 2 +- envs/env-py312.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index 1b2fd2a..cb67b89 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -35,7 +35,7 @@ jobs: needs: pre-commit strategy: matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.11", "3.12"] fail-fast: false env: TZ: America/New_York diff --git a/envs/env-py310.yml b/envs/env-py310.yml index fd394b0..8d342d2 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - # - rich >=14.1.0 + - rich # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn diff --git a/envs/env-py311.yml b/envs/env-py311.yml index dfe86a6..51ab24d 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - # - rich >=14.1.0 + - rich # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 0901ec8..cc43247 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -166,7 +166,7 @@ dependencies: - redis-py - reportlab - requests - # - rich >=14.1.0 + - rich # - sasview # does not work with pyqt>=5.15 - scikit-beam >=0.0.24 - scikit-learn From e557511c1bfaf077ad0b64c6f3393e000e49ddd5 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Mon, 8 Sep 2025 10:25:21 -0400 Subject: [PATCH 09/19] No py310 in the test job --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index cb67b89..fd3e1bd 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -208,7 +208,7 @@ jobs: repo: "tes-profile-collection" branch: "main" beamline-acronym: "tes" - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.11", "3.12"] fail-fast: false env: TZ: America/New_York From 4fe48929befda3b8c7fac597e30802b497e21f95 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Mon, 22 Sep 2025 15:21:55 -0400 Subject: [PATCH 10/19] Use the wip action version with more logging --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index fd3e1bd..b3afb7e 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -257,7 +257,7 @@ jobs: ls -la ${ARTIFACTS_DIR} - name: Test the env with the beamline integration test action - uses: NSLS2/gha-beamline-integration-test@2025-1.0-test + uses: NSLS2/gha-beamline-integration-test@2025-3.0-test with: conda_env_url: "" conda_env_md5: "${{ env.CONDA_PACK_ENV_CHECKSUM_MD5 }}" From c18963f850b105a9ca9e70ddef53501d089935d2 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Mon, 22 Sep 2025 15:46:57 -0400 Subject: [PATCH 11/19] fastapi >=0.115.8 - needed for Tiled --- envs/env-py310.yml | 1 + envs/env-py311.yml | 1 + envs/env-py312.yml | 1 + 3 files changed, 3 insertions(+) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 8d342d2..46090e8 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -59,6 +59,7 @@ dependencies: - eiger-io - event-model >=1.21 - fabio + - fastapi >=0.115.8 - ffmpeg >=4.0 - flake8 - fpdf2 diff --git a/envs/env-py311.yml b/envs/env-py311.yml index 51ab24d..8210c80 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -59,6 +59,7 @@ dependencies: - eiger-io - event-model >=1.21 - fabio + - fastapi >=0.115.8 - ffmpeg >=4.0 - flake8 - fpdf2 diff --git a/envs/env-py312.yml b/envs/env-py312.yml index cc43247..0ab72b3 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -59,6 +59,7 @@ dependencies: - eiger-io - event-model >=1.21 - fabio + - fastapi >=0.115.8 - ffmpeg >=4.0 - flake8 - fpdf2 From 94887e9c7d24867851f3e0ca7c9c06aff77605c1 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Mon, 22 Sep 2025 15:59:38 -0400 Subject: [PATCH 12/19] Remove prefect (not needed anymore) it was holding the starlette version to a much older one, not compatible with Tiled --- envs/env-py310.yml | 1 - envs/env-py311.yml | 1 - envs/env-py312.yml | 1 - 3 files changed, 3 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 46090e8..592a46d 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -132,7 +132,6 @@ dependencies: - pillow - pocl # needed by pyopencl, used by the `xrt` package - pre-commit - - prefect >=2.18,<3 - py-xgboost - py4xs - pycentroids diff --git a/envs/env-py311.yml b/envs/env-py311.yml index 8210c80..f187a47 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -132,7 +132,6 @@ dependencies: - pillow - pocl # needed by pyopencl, used by the `xrt` package - pre-commit - - prefect >=2.18,<3 - py-xgboost - py4xs - pycentroids diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 0ab72b3..6fa82a7 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -132,7 +132,6 @@ dependencies: - pillow - pocl # needed by pyopencl, used by the `xrt` package - pre-commit - - prefect >=2.18,<3 - py-xgboost - py4xs - pycentroids From afdefed7498560a89c2d85a98971adf4d3adc58a Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Tue, 30 Sep 2025 04:33:12 -0400 Subject: [PATCH 13/19] Pin tiled to >=0.1.6 --- envs/env-py310.yml | 2 +- envs/env-py311.yml | 2 +- envs/env-py312.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 592a46d..0f9dd10 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -186,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b39 + - tiled >=0.1.6 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 diff --git a/envs/env-py311.yml b/envs/env-py311.yml index f187a47..ceb78a6 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -186,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b39 + - tiled >=0.1.6 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 6fa82a7..9333de2 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -186,7 +186,7 @@ dependencies: - suitcase-tiff >=0.4.0 - suitcase-utils - sympy - - tiled >=0.1.0b39 + - tiled >=0.1.6 - toml # Latest tomopy v1.15.2 has conflicts with some packages in this environment. - tomopy >=1.12.2 From 480780353ee8794d6f5882320fb986e36930eca0 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 2 Oct 2025 18:26:49 -0400 Subject: [PATCH 14/19] CI: use the base branch `2025-1.0-test` for the `NSLS2/gha-beamline-integration-test` action --- .github/workflows/package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index b3afb7e..fd3e1bd 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -257,7 +257,7 @@ jobs: ls -la ${ARTIFACTS_DIR} - name: Test the env with the beamline integration test action - uses: NSLS2/gha-beamline-integration-test@2025-3.0-test + uses: NSLS2/gha-beamline-integration-test@2025-1.0-test with: conda_env_url: "" conda_env_md5: "${{ env.CONDA_PACK_ENV_CHECKSUM_MD5 }}" From 3ae204cf18d5ecbdb6988058aa495306d47340e3 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 2 Oct 2025 18:38:30 -0400 Subject: [PATCH 15/19] Add `numba-cuda` --- envs/env-py310.yml | 1 + envs/env-py311.yml | 1 + envs/env-py312.yml | 1 + 3 files changed, 3 insertions(+) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 0f9dd10..67cfdad 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -111,6 +111,7 @@ dependencies: - nodejs - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 + - numba-cuda - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 diff --git a/envs/env-py311.yml b/envs/env-py311.yml index ceb78a6..bdd44b2 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -111,6 +111,7 @@ dependencies: - nodejs - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 + - numba-cuda - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 9333de2..1c6ef23 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -111,6 +111,7 @@ dependencies: - nodejs - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 + - numba-cuda - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 From 225a1adabfaf02e84bdacd8660d3a2f8e140f8ca Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 2 Oct 2025 18:58:03 -0400 Subject: [PATCH 16/19] TST: add import tests for `numba-cuda` --- import-tests.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/import-tests.py b/import-tests.py index 03b1da1..b6f6104 100644 --- a/import-tests.py +++ b/import-tests.py @@ -10,6 +10,7 @@ import numexpr import larch import larch.xrd +from numba import cuda parser = argparse.ArgumentParser(description="Test import of various Python packages.") parser.add_argument( @@ -35,3 +36,4 @@ print(f"{nslsii.__version__ = }") print(f"{numexpr.__version__ = }") print(f"{larch.__version__ = }") +print(cuda.__file__) From 18053287ebd9665ee00d758c06bc421905ddb613 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 2 Oct 2025 19:00:46 -0400 Subject: [PATCH 17/19] TST: add more numba import tests --- import-tests.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/import-tests.py b/import-tests.py index b6f6104..25cf056 100644 --- a/import-tests.py +++ b/import-tests.py @@ -10,6 +10,7 @@ import numexpr import larch import larch.xrd +import numba from numba import cuda parser = argparse.ArgumentParser(description="Test import of various Python packages.") @@ -36,4 +37,5 @@ print(f"{nslsii.__version__ = }") print(f"{numexpr.__version__ = }") print(f"{larch.__version__ = }") +print(f"{numba.__version__ = }") print(cuda.__file__) From 4ff128dd5584434721d795f0c64b830c334a2ea8 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Thu, 2 Oct 2025 19:22:18 -0400 Subject: [PATCH 18/19] Use cuda-version 12 --- envs/env-py310.yml | 1 + envs/env-py311.yml | 1 + envs/env-py312.yml | 1 + 3 files changed, 3 insertions(+) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 67cfdad..6b6da44 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -112,6 +112,7 @@ dependencies: - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 - numba-cuda + - cuda-version >=12,<13 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 diff --git a/envs/env-py311.yml b/envs/env-py311.yml index bdd44b2..cdf7755 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -112,6 +112,7 @@ dependencies: - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 - numba-cuda + - cuda-version >=12,<13 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 1c6ef23..012fa89 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -112,6 +112,7 @@ dependencies: - nsls2-detector-handlers >=0.0.3 - nslsii >=0.11.4 - numba-cuda + - cuda-version >=12,<13 - numexpr >=2.8.0,!=2.8.4 - numpy >=1.20 - nyxtools >=0.0.12 From 83492c857d2cc9611890258fb95d188aef457e93 Mon Sep 17 00:00:00 2001 From: Max Rakitin Date: Fri, 3 Oct 2025 10:25:24 -0400 Subject: [PATCH 19/19] Remove `pymca` --- envs/env-py310.yml | 1 - envs/env-py311.yml | 1 - envs/env-py312.yml | 1 - 3 files changed, 3 deletions(-) diff --git a/envs/env-py310.yml b/envs/env-py310.yml index 6b6da44..aa70ea1 100644 --- a/envs/env-py310.yml +++ b/envs/env-py310.yml @@ -146,7 +146,6 @@ dependencies: - pymatgen >=2024.5.1 - maggma >=0.66 - mp-api >=0.41.2 - - pymca - pymcr - pymongo >=3.7 - pyobjcryst diff --git a/envs/env-py311.yml b/envs/env-py311.yml index cdf7755..e787976 100644 --- a/envs/env-py311.yml +++ b/envs/env-py311.yml @@ -146,7 +146,6 @@ dependencies: - pymatgen >=2024.5.1 - maggma >=0.66 - mp-api >=0.41.2 - - pymca - pymcr - pymongo >=3.7 - pyobjcryst diff --git a/envs/env-py312.yml b/envs/env-py312.yml index 012fa89..f806fbe 100644 --- a/envs/env-py312.yml +++ b/envs/env-py312.yml @@ -146,7 +146,6 @@ dependencies: - pymatgen >=2024.5.1 - maggma >=0.66 - mp-api >=0.41.2 - - pymca - pymcr - pymongo >=3.7 - pyobjcryst