chore: replace Codacy with in-repo tooling

.github/workflows/lint.yml

@@ -0,0 +1,37 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+jobs:
+  lint:
+    name: ruff + black
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      # --output-format=github renders findings as inline PR annotations,
+      # which is the part of the Codacy integration worth keeping.
+      - name: Run ruff
+        run: uv run ruff check --output-format=github src tests
+
+      - name: Run black
+        run: uv run black --check --diff src tests

.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+# Keep ruff and black revs in step with the versions in the dev extra of
+# pyproject.toml. Drift between them produces the "passes locally, fails in
+# CI" failure mode.
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.11
+    hooks:
+      - id: ruff-check
+        # No --fix: this package uses deliberate registration-only imports
+        # (e.g. models/proposal.py's `partner # noqa: F401`) that F401's
+        # autofix would silently delete. Report-only also matches the
+        # check-only Lint workflow.
+        # Match the Lint workflow, which checks src and tests only.
+        # alembic/ migrations are historical and deliberately unlinted.
+        files: ^(src|tests)/
+
+  - repo: https://github.com/psf/black
+    rev: 25.12.0
+    hooks:
+      - id: black
+        files: ^(src|tests)/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        # Vendored Bokeh-generated HTML fixtures; rewriting them on every
+        # regeneration produces a phantom whitespace-only diff.
+        exclude: ^examples/data/uploader/
+      - id: end-of-file-fixer
+        # Same vendored fixtures as trailing-whitespace above.
+        exclude: ^examples/data/uploader/
+      - id: check-yaml
+        # mkdocs-material's config uses !!python/name: tags, which
+        # yaml.safe_load cannot construct.
+        exclude: ^mkdocs\.yml$
+      - id: check-toml
+      - id: check-added-large-files
+        # Uploader example fixtures (e.g. ppp_figure_*.html) legitimately
+        # exceed the default 500kb limit and are committed on purpose.
+        exclude: ^examples/data/uploader/

README.md

@@ -81,6 +81,17 @@ If you want to install the package under the Python library directory, you can e
 
 The installation process will install some command-line tools under the directory where your Python executable is located.
 
+### Development setup
+
+If you are going to contribute, install the development dependencies and enable the pre-commit hooks:
+
+```console
+python3 -m pip install -e ".[dev]"
+pre-commit install
+```
+
+The hooks run `ruff` and `black` on the files you stage, plus whitespace and syntax checks. CI runs `ruff` and `black` over all of `src` and `tests`; run `pre-commit run --all-files` to check the whole tree the way CI does.
+
 
 ## Usage Examples
 

alembic/local_test/alembic/README

@@ -1 +1 @@
-Generic single-database configuration.
+Generic single-database configuration.

alembic/local_test/alembic/versions/6407841f5938_baseline.py

@@ -1,7 +1,7 @@
 """baseline
 
 Revision ID: 6407841f5938
-Revises: 
+Revises:
 Create Date: 2022-05-11 16:21:57.324356
 
 """

alembic/pfsa-db01-gb/alembic/versions/20220512-103708_33e97fab1034_initial_revision.py

@@ -1,7 +1,7 @@
 """initial revision
 
 Revision ID: 33e97fab1034
-Revises: 
+Revises:
 Create Date: 2022-05-12 10:37:08.039899
 
 """

alembic/pfsa-db01-gb/alembic/versions/20240417-100959_c636e8e2ecc0_add_unique_constraint_on_the_sky_table.py

@@ -4,7 +4,7 @@
 Revises: 065b74905fb6
 Create Date: 2024-04-17 10:09:59.291914
 
-Note: 
+Note:
 Before upgrading the database, I run the following query to avoid the violation of the unique constaint:
 ```
 UPDATE sky SET obj_id = sky_id WHERE version = '20220915';

alembic/pfsa-db01-gb/alembic/versions/20250801-202638_89865530fdf1_add_index_in_obj_id_input_catalog_id_.py

@@ -1,4 +1,4 @@
-"""add index in obj_id, input_catalog_id, and proposal_id for target table 
+"""add index in obj_id, input_catalog_id, and proposal_id for target table
 
 Revision ID: 89865530fdf1
 Revises: 3923581e4392

docs/examples/index.md

@@ -6,4 +6,4 @@ Some simple examples to work with `targetdb` are provided as follows.
 - [Preparation of input data](preparation.md): how to prepare input data for `targetdb`.
 - [Useful queries](queries.md): useful queries to work with `targetdb`.
 - [Run `targetdb` in a Docker container](docker.md): how to run `targetdb` in a Docker container.
-- [Tutorial on preparing PFS openuse](obsproc.md): Workflow to prepare the database content for PFS openuse observations.
+- [Tutorial on preparing PFS openuse](obsproc.md): Workflow to prepare the database content for PFS openuse observations.

docs/reference/api.md

@@ -1,3 +1,3 @@
 # API Reference
 
-TBD
+TBD

docs/tbls/public.fluxstd.md

@@ -101,10 +101,10 @@
 | ---- | ---------- |
 | fluxstd_pkey | CREATE UNIQUE INDEX fluxstd_pkey ON public.fluxstd USING btree (fluxstd_id) |
 | uq_obj_id_input_catalog_id_version | CREATE UNIQUE INDEX uq_obj_id_input_catalog_id_version ON public.fluxstd USING btree (obj_id, input_catalog_id, version) |
-| ix_fluxstd_input_catalog_fluxstdid | CREATE INDEX ix_fluxstd_input_catalog_fluxstdid ON public.fluxstd USING btree (input_catalog_id, fluxstd_id) |
 | ix_fluxstd_version_fluxstdid | CREATE INDEX ix_fluxstd_version_fluxstdid ON public.fluxstd USING btree (version, fluxstd_id) |
-| fluxstd_q3c_ang2ipix_idx | CREATE INDEX fluxstd_q3c_ang2ipix_idx ON public.fluxstd USING btree (q3c_ang2ipix(ra, "dec")) |
 | ix_fluxstd_version | CREATE INDEX ix_fluxstd_version ON public.fluxstd USING btree (version) |
+| fluxstd_q3c_ang2ipix_idx | CREATE INDEX fluxstd_q3c_ang2ipix_idx ON public.fluxstd USING btree (q3c_ang2ipix(ra, "dec")) |
+| ix_fluxstd_input_catalog_fluxstdid | CREATE INDEX ix_fluxstd_input_catalog_fluxstdid ON public.fluxstd USING btree (input_catalog_id, fluxstd_id) |
 
 ## Relations
 

docs/tbls/public.target.md

@@ -121,11 +121,11 @@
 | target_pkey | CREATE UNIQUE INDEX target_pkey ON public.target USING btree (target_id) |
 | target_propid_obcode_catid_objid_resolution_key | CREATE UNIQUE INDEX target_propid_obcode_catid_objid_resolution_key ON public.target USING btree (proposal_id, ob_code, input_catalog_id, obj_id, is_medium_resolution) |
 | target_propid_obcode_key | CREATE UNIQUE INDEX target_propid_obcode_key ON public.target USING btree (proposal_id, ob_code) |
+| target_q3c_ang2ipix_idx | CREATE INDEX target_q3c_ang2ipix_idx ON public.target USING btree (q3c_ang2ipix(ra, "dec")) |
 | target_proposal_id_idx | CREATE INDEX target_proposal_id_idx ON public.target USING btree (proposal_id) |
 | target_obj_id_input_catalog_id_idx | CREATE INDEX target_obj_id_input_catalog_id_idx ON public.target USING btree (obj_id, input_catalog_id) |
 | target_input_catalog_id_idx | CREATE INDEX target_input_catalog_id_idx ON public.target USING btree (input_catalog_id) |
 | target_proposal_id_obj_id_idx | CREATE INDEX target_proposal_id_obj_id_idx ON public.target USING btree (proposal_id, obj_id) |
-| target_q3c_ang2ipix_idx | CREATE INDEX target_q3c_ang2ipix_idx ON public.target USING btree (q3c_ang2ipix(ra, "dec")) |
 
 ## Relations
 

examples/data/filter_names.csv

@@ -18,4 +18,4 @@ u_sdss,SDSS u filter
 g_sdss,SDSS g filter
 r_sdss,SDSS r filter
 i_sdss,SDSS i filter
-z_sdss,SDSS z filter
+z_sdss,SDSS z filter

examples/data/input_catalogs.csv

@@ -15,4 +15,4 @@ input_catalog_id,input_catalog_name,input_catalog_description,upload_id
 1001,sky_hscssp_s21a_wide,Sky positions from S21A HSC-SSP (Wide),
 1002,sky_s1,Sky positions from PS1,
 1003,sky_gaia,Sky positions from Gaia,
-1004,sky_nops1,Sky postionns for regions without PS1 data,
+1004,sky_nops1,Sky postionns for regions without PS1 data,

examples/data/proposals.csv

@@ -35,4 +35,4 @@ S24B-QT910,o00010,Wanqiu,He,NaN,7.5,B,5307.25,5307.25,0.0,1,subaru,False
 S24B-QT911,o00011,Mao,Zhiying,NaN,10.0,A,5348.05,5348.05,0.0,1,subaru,False
 S24B-QT912,o00012,Yuki,Moritani,NaN,9.5,A,350.25,350.25,0.0,1,subaru,False
 S24B-QT913,o00013,Vera,Passegger,Maria,7.0,B,263.0,263.0,0.0,1,subaru,False
-S24B-QT914,o00014,Miho,Ishigaki,NaN,0.0,F,0.0,0.0,0.0,1,subaru,False
+S24B-QT914,o00014,Miho,Ishigaki,NaN,0.0,F,0.0,0.0,0.0,1,subaru,False

examples/data/targets/example_input_catalogs_current.csv

@@ -1,2 +1 @@
 input_catalog_name,input_catalog_description,upload_id,proposal_id,is_classical,is_user_pointing
-