Merge remote-tracking branch 'origin/main' into 2024-05/some-gwr

.gitattributes

@@ -0,0 +1,4 @@
+# Mark generated protobuf files to be collapsed by default in PRs
+# See: https://docs.github.com/en/repositories/working-with-files/managing-files/customizing-how-changed-files-appear-on-github
+*_pb2.py        linguist-generated=true
+*_pb2.pyi       linguist-generated=true

.github/workflows/ci.yaml

@@ -32,7 +32,7 @@ jobs:
           pip install -r dev_tools/requirements/envs/pytest.env.txt
           pip install --no-deps -e .
       - run: |
-          check/pytest -m 'not notebooks'
+          check/pytest -m 'not notebook and not slow'
 
   pytest-dev-tools:
     runs-on: ubuntu-latest
@@ -99,7 +99,7 @@ jobs:
           pip install --no-deps -e .
       - run: |
           check/pylint
-  
+
   mypy:
     runs-on: ubuntu-latest
     steps:
@@ -116,3 +116,19 @@ jobs:
           pip install --no-deps -e .
       - run: |
           check/mypy
+
+  autogenerate-notebooks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ts-graphviz/setup-graphviz@v1
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev_tools/requirements/envs/docs.env.txt
+          pip install --no-deps -e .
+      - run: |
+          check/autogenerate-notebooks

.github/workflows/tests.yaml

@@ -0,0 +1,34 @@
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+name: Nightly tests
+
+on:
+  schedule:
+    - cron: "0 11 * * 1-5"  # Mon-Fri at 11:00 AM UTC
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ts-graphviz/setup-graphviz@v1
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev_tools/requirements/envs/pytest.env.txt
+          pip install --no-deps -e .
+      - run: |
+          check/pytest

.gitignore

@@ -134,4 +134,7 @@ dmypy.json
 # files that get generated when testing
 mod_exp_bloq.json
 mod_exp_cbloq.json
-musical_score_example.json
+musical_score_example.json
+
+# Jupyter
+jupyter_kernel.lock

check/autogenerate-notebooks

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+################################################################################
+# Autogenerates the notebooks and reports whether there were any changes.
+#
+# Usage:
+#     check/autogenerate-notebooks
+#
+################################################################################
+
+python dev_tools/autogenerate-bloqs-notebooks-v2.py || exit $?
+
+if output=$(git status --porcelain) && [ -z "$output" ]; then
+  # Working directory clean
+  exit 0
+else
+  # Uncommitted changes
+  echo $output
+  exit 1
+fi

check/pylint-changed-files

@@ -46,16 +46,16 @@ else
     echo -e "\033[31mNo default revision found to compare against. Argument #1 must be what to diff against (e.g. 'origin/main' or 'HEAD~1').\033[0m" >&2
     exit 1
 fi
-base="$(git merge-base ${rev} HEAD)"
-if [ "$(git rev-parse ${rev})" == "${base}" ]; then
+base="$(git merge-base "${rev}" HEAD)"
+if [ "$(git rev-parse "${rev}")" == "${base}" ]; then
     echo -e "Comparing against revision '${rev}'." >&2
 else
     echo -e "Comparing against revision '${rev}' (merge base ${base})." >&2
     rev="${base}"
 fi
 
 typeset -a changed
-IFS=$'\n' read -r -d '' -a changed < <(git diff --name-only "${rev}" -- '*.py')
+IFS=$'\n' read -r -d '' -a changed < <(git diff --diff-filter=d --name-only "${rev}" -- '*.py')
 
 num_changed=${#changed[@]}