Minor bug fixes

.github/workflows/ci-python.yml

@@ -26,12 +26,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: astral-sh/ruff-action@v3
+      - uses: astral-sh/ruff-action@0ce1b0bf8b818ef400413f810f8a11cdbda0034b # v4.0.0
         with:
           version: "latest"
           args: "check"
           src: "./compass"
-      - uses: astral-sh/ruff-action@v3
+      - uses: astral-sh/ruff-action@0ce1b0bf8b818ef400413f810f8a11cdbda0034b # v4.0.0
         with:
           version: "latest"
           args: "format --check"
@@ -52,7 +52,7 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: prefix-dev/[email protected]
+    - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
       with:
         pixi-version: v0.62.2
         locked: true
@@ -81,7 +81,7 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: prefix-dev/[email protected]
+    - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
       with:
         pixi-version: v0.62.2
         locked: true
@@ -110,7 +110,7 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: prefix-dev/[email protected]
+    - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
       with:
         pixi-version: v0.62.2
         locked: true
@@ -141,14 +141,14 @@ jobs:
 
     - name: Set up Python  ${{ matrix.python-version }} (with cache)
       if: github.ref == 'refs/heads/main'
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
 
     - name: Set up Python  ${{ matrix.python-version }} (no cache)
       if: github.ref != 'refs/heads/main'
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -172,7 +172,7 @@ jobs:
         python -m pip install pdftotext
 
     - name: Load tox cache
-      uses: actions/cache/restore@v5
+      uses: actions/cache/restore@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
       with:
         path: .tox/
         key: ${{ runner.os }}-${{ matrix.python-version }}-tox-v1-${{ hashFiles('**/pyproject.toml') }}
@@ -186,7 +186,7 @@ jobs:
 
     - name: Save tox cache only on main
       if: github.ref == 'refs/heads/main'
-      uses: actions/cache/save@v5
+      uses: actions/cache/save@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
       with:
         path: .tox/
         key: ${{ runner.os }}-${{ matrix.python-version }}-tox-v1-${{ hashFiles('**/pyproject.toml') }}

.github/workflows/ci-rust.yml

@@ -32,15 +32,15 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           # Don't save cache for cargo check!
@@ -59,15 +59,15 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           # Don't save cache for cargo fmt or clippy!
@@ -94,15 +94,15 @@ jobs:
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           save-if: ${{ github.ref == 'refs/heads/main' }}
@@ -127,15 +127,15 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           save-if: false
@@ -158,15 +158,15 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           save-if: false
@@ -187,15 +187,15 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           frozen: true
           cache: true
           cache-write: ${{ github.ref == 'refs/heads/main' }}
           environments: rdev
 
-      - uses: Swatinem/rust-cache@v2
+      - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # v2.9.1
         with:
           shared-key: "gha"
           save-if: false

.github/workflows/codecov.yml

@@ -30,7 +30,7 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: prefix-dev/[email protected]
+    - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
       with:
         pixi-version: v0.62.2
         locked: true
@@ -44,7 +44,7 @@ jobs:
         pixi run -e pdev --locked tests-p
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v6
+      uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml

.github/workflows/codeql.yml

@@ -33,12 +33,12 @@ jobs:
       uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4
+      uses: github/codeql-action/init@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4
+      uses: github/codeql-action/analyze@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/docs.yml

@@ -1,6 +1,7 @@
 name: Release Documentation
 
-permissions: write-all
+permissions:
+  contents: write
 
 on:
   pull_request:
@@ -34,7 +35,7 @@ jobs:
           fetch-depth: 0
           fetch-tags: true
 
-      - uses: prefix-dev/[email protected]
+      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
         with:
           pixi-version: v0.62.2
           locked: true
@@ -45,7 +46,7 @@ jobs:
         run: pixi run -e pdoc python-docs  # This errors on warnings
 
       - name: deploy
-        uses: peaceiris/[email protected]
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
         if: startsWith(github.ref, 'refs/tags/v')
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish_to_pypi.yml

@@ -21,7 +21,7 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: prefix-dev/[email protected]
+    - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5
       with:
         pixi-version: v0.62.2
         locked: true
@@ -32,4 +32,5 @@ jobs:
       run: pixi run -e pbuild build-wheels
 
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.14.0
+

.github/workflows/release-cli.yml

@@ -6,9 +6,14 @@ on:
       - 'c*.*.*'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   publish:
     name: ${{ matrix.target }}
+    permissions:
+      contents: write
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -38,7 +43,7 @@ jobs:
     - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Install Rust
-      uses: actions-rs/toolchain@v1
+      uses: actions-rs/toolchain@16499b5e05bf2e26879000db0c1d13f7e13fa3af # v1.0.6
       with:
         toolchain: stable
         profile: minimal
@@ -62,7 +67,7 @@ jobs:
         fi
 
     - name: Build
-      uses: actions-rs/cargo@v1
+      uses: actions-rs/cargo@844f36862e911db73fe0815f00a4a2602c279505 # v1.0.6
       with:
         use-cross: ${{ matrix.use-cross }}
         command: build
@@ -73,7 +78,7 @@ jobs:
       run: ${{ matrix.strip }} target/${{ matrix.target }}/release/infra-compass-cli${{ matrix.binary_ext }}
 
     - name: Upload binaries to release
-      uses: svenstaro/upload-release-action@v2
+      uses: svenstaro/upload-release-action@29e53e917877a24fad85510ded594ab3c9ca12de # v2.11.5
       with:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
         file: target/${{ matrix.target }}/release/infra-compass-cli${{ matrix.binary_ext }}

compass/_cli/finalize.py

@@ -19,10 +19,10 @@
     "-c",
     required=True,
     type=click.Path(exists=True),
-    help="Path to ordinance configuration JSON or JSON5 file. This file "
+    help="Path to COMPASS run configuration JSON or JSON5 file. This file "
     "should contain any/all the arguments to pass to "
-    ":func:`compass.scripts.process.process_jurisdictions_with_openai`."
-    "The directory that this config points to will be finalized.",
+    ":func:`compass.scripts.process.process_jurisdictions_with_openai`. "
+    "The output directory that this config points to will be finalized.",
 )
 def finalize(config):
     """Finalize a partially-completed COMPASS run"""

compass/extraction/water/plugin.py

@@ -248,7 +248,7 @@ def save_structured_data(cls, doc_infos, out_dir):
         """
         db = []
         for doc_info in doc_infos:
-            ord_db = pd.read_csv(doc_info["ord_db_fp"])
+            ord_db = pd.read_csv(doc_info["ord_db_fp"], encoding="utf-8-sig")
             if len(ord_db) == 0:
                 continue
 
@@ -265,7 +265,11 @@ def save_structured_data(cls, doc_infos, out_dir):
             return 0
 
         db = pd.concat([df.dropna(axis=1, how="all") for df in db], axis=0)
-        db.to_csv(Path(out_dir) / "water_rights.csv", index=False)
+        db.to_csv(
+            Path(out_dir) / "water_rights.csv",
+            index=False,
+            encoding="utf-8-sig",
+        )
         return len(db["WCD_ID"].unique())
 
 

compass/services/threaded.py

@@ -98,7 +98,7 @@ def _write_ord_db(extraction_context, out_dir, out_fn=None):
         return None
 
     out_fp = Path(out_dir) / out_fn
-    ord_db.to_csv(out_fp, index=False)
+    ord_db.to_csv(out_fp, index=False, encoding="utf-8-sig")
     return out_fp
 
 

compass/utilities/finalize.py

@@ -172,7 +172,7 @@ def doc_infos_to_db(doc_infos):
         if ord_db_fp is None:
             continue
 
-        ord_db = pd.read_csv(ord_db_fp)
+        ord_db = pd.read_csv(ord_db_fp, encoding="utf-8-sig")
 
         if num_ordinances_dataframe(ord_db) == 0:
             continue
@@ -217,8 +217,16 @@ def save_db(db, out_dir):
     out_dir = Path(out_dir)
     qual_db = db[~db["quantitative"]][QUAL_OUT_COLS]
     quant_db = db[db["quantitative"]][QUANT_OUT_COLS]
-    qual_db.to_csv(out_dir / "qualitative_ordinances.csv", index=False)
-    quant_db.to_csv(out_dir / "quantitative_ordinances.csv", index=False)
+    qual_db.to_csv(
+        out_dir / "qualitative_ordinances.csv",
+        index=False,
+        encoding="utf-8-sig",
+    )
+    quant_db.to_csv(
+        out_dir / "quantitative_ordinances.csv",
+        index=False,
+        encoding="utf-8-sig",
+    )
 
 
 def _db_results(results, jurisdiction):

docs/source/_cli/cli.rst

@@ -1,9 +1,8 @@
 .. _cli-docs:
 
 Command Line Interface (CLI)
-==============================
+============================
 
 .. toctree::
 
    compass
-   compass process