july update

.clang-format

@@ -6,3 +6,8 @@ BinPackArguments: false
 BinPackParameters: false
 AccessModifierOffset: -4
 ReflowComments: false
+AlignTrailingComments:
+  Kind: Always
+  OverEmptyLines: 2
+FixNamespaceComments: true
+PointerAlignment: Right

.dockerignore

@@ -3,18 +3,19 @@
 **/.Python/
 **/build/
 **/dist/
-*.egg-info/
+**/*.egg-info/
 **/.coverage/
+**/coverage/
 **/.ipynb_checkpoints*/
-**/attic/
 **/examples/
-**/coverage/
+**/tests/
 **/.pytest*
 **/.mypy*
 **/.clang*
+**/.hypothesis/
 Dockerfile
 .dockerignore
-
+.gitlab-ci.yml
 
 # Git Files
 **/.git*
@@ -36,3 +37,7 @@ oe_license.txt
 *.svg
 *.pkl
 *.png
+
+# nsys files
+**/*.nsys-rep
+**/*.sqlite

.git-blame-ignore-revs

@@ -31,3 +31,6 @@ e21cbb8f048840dc24723b60ca3351dbeac8d207
 
 # Normalize numpy vs. jax.numpy imports
 1d49b8f5159d8454e0d14daa441bbade01a3dc4d
+
+# Apply formatting changes from switch to ruff
+a882ce08ddc00fb3a6b3dd2a28b2f1ff6a7d9829

.gitignore

@@ -8,8 +8,10 @@ oe_license.txt
 *.swp
 .ipynb_checkpoints/
 build/
+dist/
 *.egg-info/
 .coverage*
+.hypothesis/
 
 # Nsys profiling files
 *.sqlite

.gitlab-ci.yml

@@ -19,28 +19,26 @@ workflow:
 
 docker_build:
   stage: build-docker
-  image: docker:20.10
+  image: docker:27.3.1
   tags:
-    - gpu
-    - docker
+    - aws-tardis-gpu
   script:
     - DOCKER_HOST=tcp://localhost:2375 docker login -u $CI_REGISTRY_USER -p $CI_JOB_TOKEN $CI_REGISTRY
-    # Prune images older than 2 days
-    - docker system prune --filter "until=48h" -f -a
     # Pull the docker containers
-    - docker pull $CI_REGISTRY_IMAGE:$CI_DEFAULT_BRANCH || true
-    - docker pull $DOCKER_TAG || true
+    - docker pull $DOCKER_TAG || docker pull $CI_REGISTRY_IMAGE:$CI_DEFAULT_BRANCH || true
     # Cache from default branch and most recent image to get most out of the caching
-    - docker build -t $DOCKER_TAG --cache-from $CI_REGISTRY_IMAGE:$CI_DEFAULT_BRANCH,$DOCKER_TAG --target timemachine_ci .
+    - docker build -t $DOCKER_TAG --cache-from $DOCKER_TAG --cache-from $CI_REGISTRY_IMAGE:$CI_DEFAULT_BRANCH --cache-to type=inline --target timemachine_ci .
     - docker push $DOCKER_TAG
 
 lint:
   stage: lint
   image: $DOCKER_TAG
   needs: ["docker_build"]
+  # Specify cuda arch, so that a GPU is not required to detect the cuda arch.
+  variables:
+    CUDA_ARCH: 75
   tags:
-    - timemachine
-    - gpu
+    - aws-tardis-cpu
   rules:
     - if: $CI_EXTERNAL_PULL_REQUEST_IID
     - if: $NIGHTLY_TESTS
@@ -52,8 +50,7 @@ nocuda-tests:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - timemachine
-    - cpu
+    - aws-tardis-cpu
   rules:
     - if: $CI_EXTERNAL_PULL_REQUEST_IID
   script:
@@ -66,13 +63,34 @@ nocuda-tests:
     when: on_success
     expire_in: 1 week
 
+packaging:
+  stage: lint
+  image: $DOCKER_TAG
+  needs: ["docker_build"]
+  tags:
+    - aws-tardis-cpu
+  rules:
+    - if: $CI_EXTERNAL_PULL_REQUEST_IID
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+  # Specify cuda arch, so that a GPU is not required to detect the cuda arch.
+  variables:
+    CMAKE_ARGS: -DCUDA_ARCH=75
+  script:
+    - pip install build==1.2.2.post1
+    - python -m build --sdist
+    - pip install dist/timemachine-*.tar.gz
+  artifacts:
+    name: "$CI_JOB_NAME-$CI_COMMIT_REF_NAME-packaging"
+    paths:
+        - dist/
+    expire_in: 1 week
+
 nogpu-tests:
   stage: test
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - timemachine
-    - cpu
+    - aws-tardis-cpu
   rules:
     - if: $CI_EXTERNAL_PULL_REQUEST_IID
   # Build custom ops with fixed cuda arch, to test C++ that is CPU only
@@ -93,7 +111,7 @@ memory-tests:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - gpu
+    - aws-tardis-gpu
   rules:
     - if: $CI_EXTERNAL_PULL_REQUEST_IID
   script:
@@ -111,7 +129,7 @@ unit-tests:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - gpu
+    - aws-tardis-gpu
   rules:
     - if: $CI_EXTERNAL_PULL_REQUEST_IID
   script:
@@ -129,7 +147,7 @@ nightly-tests:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - gpu
+    - aws-tardis-gpu
   rules:
     - if: $NIGHTLY_TESTS
   script:
@@ -147,7 +165,7 @@ nightly-memcheck-tests:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - gpu
+    - aws-tardis-gpu
   rules:
     - if: $NIGHTLY_TESTS
   script:
@@ -165,8 +183,7 @@ nightly-tests-nocuda:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - timemachine
-    - cpu
+    - aws-tardis-cpu
   rules:
     - if: $NIGHTLY_TESTS
   script:
@@ -184,8 +201,7 @@ nightly-tests-nogpu:
   image: $DOCKER_TAG
   needs: ["lint"]
   tags:
-    - timemachine
-    - cpu
+    - aws-tardis-cpu
   rules:
     - if: $NIGHTLY_TESTS
   # Build custom ops with fixed cuda arch, to test C++ that is CPU only

.pre-commit-config.yaml

@@ -1,45 +1,35 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: isort
-        name: isort (python)
-
--   repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-    -   id: black
-
--   repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-    -   id: flake8
-        exclude: '^timemachine/cpp'
+    -   id: ruff
+        args: [ --fix ]
+    -   id: ruff-format
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.14.1
     hooks:
     -   id: mypy
         # include dependencies that export types (i.e. have a py.typed file in the root module) so that they can be used
         # by mypy in pre-commit
         additional_dependencies:
-          - "jax==0.4.14"
-          - "numpy==1.23.5"
-          - "scipy==1.10.1"
-          - "matplotlib==3.7.1"
+          - "jax==0.4.28"
+          - "numpy==2.2.2"
+          - "scipy==1.15.1"
+          - "matplotlib==3.10.0"
 
         # Exclude custom_ops.py to work around clash with stub file when typechecking
         exclude: '^timemachine/lib/custom_ops.py$'
 
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v16.0.6
+    rev: v19.1.7
     hooks:
     -   id: clang-format
         types_or: [c, c++, cuda]
@@ -59,16 +49,14 @@ repos:
         pass_filenames: false
         files: '^timemachine/cpp/src/wrap_kernels.cpp$'
 
-exclude: >
-  (?x)
+exclude: |
+  (?x)(
     \.pdb$
   | \.sdf$
   | \.proto$
   | \.xml$
   | /vendored/
-  | ^attic/
   | ^timemachine/ff/params/
   | ^timemachine/_vendored/
-  | ^versioneer\.py$
-  | ^timemachine/_version\.py$
   | ^timemachine/lib/custom_ops.pyi$
+  )