Merge pull request #129 from sul-dlss/update-uv

Update to uv and airflow

.github/workflows/test.yml

@@ -27,13 +27,11 @@ jobs:
         with:
           args: 'format --check'
 
-      - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
+      - name: Install uv
+        run: pip3 install uv
 
       - name: Run tests
-        run: pytest
+        run: uv run pytest
         env:
           AIRFLOW_VAR_DIMENSIONS_API_USER: ${{ secrets.AIRFLOW_VAR_DIMENSIONS_API_USER }}
           AIRFLOW_VAR_DIMENSIONS_API_PASS: ${{ secrets.AIRFLOW_VAR_DIMENSIONS_API_PASS }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM apache/airflow:2.9.3-python3.12
+FROM apache/airflow:2.10.4-python3.12
 
 USER root
 RUN apt-get update && apt-get install -y gcc git
@@ -8,6 +8,7 @@ ENV PYTHONPATH "${PYTHONPATH}:/opt/airflow/"
 USER airflow
 
 COPY rialto_airflow ./rialto_airflow
-COPY requirements.txt ./
+
+COPY requirements.txt .
 
 RUN uv pip install --no-cache "apache-airflow==${AIRFLOW_VERSION}" -r requirements.txt

README.md

@@ -67,28 +67,10 @@ https://sul-rialto-dev.stanford.edu/authors?action=index&commit=Search&controlle
 ### Set-up
 
 1. Install `uv` for dependency management as described in [the uv docs](https://github.com/astral-sh/uv?tab=readme-ov-file#getting-started).
-2. Create a virtual environment:
-```
-uv venv
-```
-
-This will create the virtual environment at the default location of `.venv/`. `uv` automatically looks for a venv at this location when installing dependencies.
-
-3. Activate the virtual environment:
-```
-source .venv/bin/activate
-```
-
-
-### Install dependencies
-```
-uv pip install -r requirements.txt
-```
 
 To add a dependency:
-1. `uv pip install flask`
-2. Add the dependency to `pyproject.toml`.
-3. To re-generate the locked dependencies in `requirements.txt`:
+1. `uv add flask`
+3. Then re-generate the locked dependencies in `requirements.txt` which is used in `Dockerfile`.
 ```
 uv pip compile pyproject.toml -o requirements.txt
 ```
@@ -103,29 +85,15 @@ uv pip compile pyproject.toml -o requirements.txt --upgrade
 
 ## Run Tests
 
-First enable the virtual environment:
-
-```
-source .venv/bin/activate
-```
-
-Then ensure the app dependencies and dev dependencies are installed.
-
-```
-uv pip install -r requirements.txt -r requirements-dev.txt
-```
-
-Then run the tests:
-
 ```
-pytest
+uv run pytest
 ```
 
 ### Linting and formatting
 
-1. Run linting: `ruff check`
-2. Automatically fix linting: `ruff check --fix`
-3. Run formatting: `ruff format` (or `ruff format --check` to identify any unformatted files)
+1. Run linting: `uv run ruff check`
+2. Automatically fix linting: `uv run ruff check --fix`
+3. Run formatting: `uv run ruff format` (or `uv run ruff format --check` to identify any unformatted files)
 
 ## Deployment
 

pyproject.toml

@@ -1,23 +1,34 @@
 [project]
 name = "rialto-airflow"
+
 version = "0.1.0"
+
 description = "Airflow app for harvesting data for open access analysis and research intelligence."
+
 authors = [ {name = "Laura Wrubel", email = "[email protected]"}, {name = "Ed Summers", email = "[email protected]"}, {name = "Jacob Hill", email = "[email protected]"}]
-requires-python = ">= 3.12"
+
+# Aligned with what is defined in Dockerfile and CI
+requires-python = "== 3.12.*" 
+
+package-mode = false
+
 dependencies = [
     "pandas",
     "requests",
     "python-dotenv",
     "dimcli",
     "polars>=1.2",
     "pyalex",
-    "more-itertools"
+    "more-itertools",
 ]
 
 [tool.pytest.ini_options]
 pythonpath = ["."]
 addopts = "-v"
 
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+    "python-dotenv>=1.0.1",
+    "ruff>=0.9.4",
+]

requirements.txt

@@ -1,74 +1,74 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml -o requirements.txt
-alabaster==0.7.16
+alabaster==1.0.0
     # via sphinx
-asttokens==2.4.1
+asttokens==3.0.0
     # via stack-data
-babel==2.15.0
+babel==2.17.0
     # via sphinx
-certifi==2024.7.4
+certifi==2025.1.31
     # via requests
-charset-normalizer==3.3.2
+charset-normalizer==3.4.1
     # via requests
-click==8.1.7
+click==8.1.8
     # via dimcli
 commonmark==0.9.1
     # via recommonmark
 decorator==5.1.1
     # via ipython
-dimcli==1.3
+dimcli==1.4
     # via rialto-airflow (pyproject.toml)
 docutils==0.21.2
     # via
     #   recommonmark
     #   sphinx
-executing==2.0.1
+executing==2.2.0
     # via stack-data
-idna==3.7
+idna==3.10
     # via requests
 imagesize==1.4.1
     # via sphinx
-ipython==8.26.0
+ipython==8.32.0
     # via dimcli
-jedi==0.19.1
+jedi==0.19.2
     # via ipython
-jinja2==3.1.4
+jinja2==3.1.5
     # via sphinx
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
 matplotlib-inline==0.1.7
     # via ipython
-more-itertools==10.3.0
+more-itertools==10.6.0
     # via rialto-airflow (pyproject.toml)
-numpy==2.0.1
+numpy==2.2.2
     # via
     #   dimcli
     #   pandas
-packaging==24.1
+packaging==24.2
     # via
     #   dimcli
     #   sphinx
-pandas==2.2.2
+pandas==2.2.3
     # via
     #   rialto-airflow (pyproject.toml)
     #   dimcli
 parso==0.8.4
     # via jedi
 pexpect==4.9.0
     # via ipython
-polars==1.2.1
+polars==1.21.0
     # via rialto-airflow (pyproject.toml)
-prompt-toolkit==3.0.47
+prompt-toolkit==3.0.50
     # via
     #   dimcli
     #   ipython
 ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
-pyalex==0.14
+pyalex==0.15.1
     # via rialto-airflow (pyproject.toml)
-pygments==2.18.0
+pygments==2.19.1
     # via
     #   dimcli
     #   ipython
@@ -77,7 +77,7 @@ python-dateutil==2.9.0.post0
     # via pandas
 python-dotenv==1.0.1
     # via rialto-airflow (pyproject.toml)
-pytz==2024.1
+pytz==2025.1
     # via pandas
 recommonmark==0.7.1
     # via dimcli
@@ -87,37 +87,35 @@ requests==2.32.3
     #   dimcli
     #   pyalex
     #   sphinx
-six==1.16.0
-    # via
-    #   asttokens
-    #   python-dateutil
+six==1.17.0
+    # via python-dateutil
 snowballstemmer==2.2.0
     # via sphinx
-sphinx==7.4.7
+sphinx==8.1.3
     # via recommonmark
-sphinxcontrib-applehelp==1.0.8
+sphinxcontrib-applehelp==2.0.0
     # via sphinx
-sphinxcontrib-devhelp==1.0.6
+sphinxcontrib-devhelp==2.0.0
     # via sphinx
-sphinxcontrib-htmlhelp==2.0.6
+sphinxcontrib-htmlhelp==2.1.0
     # via sphinx
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
-sphinxcontrib-qthelp==1.0.8
+sphinxcontrib-qthelp==2.0.0
     # via sphinx
-sphinxcontrib-serializinghtml==1.1.10
+sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 stack-data==0.6.3
     # via ipython
-tqdm==4.66.4
+tqdm==4.67.1
     # via dimcli
 traitlets==5.14.3
     # via
     #   ipython
     #   matplotlib-inline
-tzdata==2024.1
+tzdata==2025.1
     # via pandas
-urllib3==2.2.2
+urllib3==2.3.0
     # via
     #   pyalex
     #   requests

rialto_airflow/harvest/openalex.py

@@ -3,7 +3,6 @@
 import os
 import pickle
 import time
-from urllib.parse import quote
 
 from more_itertools import batched
 from pyalex import Authors, Works, config, api
@@ -92,7 +91,7 @@ def publications_from_dois(dois: list):
         # TODO: do we need this to stay within 100,000 requests / day API quota?
         time.sleep(1)
 
-        doi_list = quote("|".join([doi for doi in doi_batch]))
+        doi_list = "|".join([doi for doi in doi_batch])
         try:
             for page in Works().filter(doi=doi_list).paginate(per_page=200):
                 for pub in page:
@@ -124,6 +123,7 @@ def normalize_publication(pub) -> dict:
 
 FIELDS = [
     "abstract_inverted_index",
+    "abstract_inverted_index_v3",
     "authorships",
     "apc_list",
     "apc_paid",

test/harvest/test_contribs.py

@@ -45,9 +45,9 @@ def test_create_contribs(pubs_parquet, doi_sunet, authors, tmp_path):
     create_contribs(pubs_parquet, doi_sunet, authors, contribs_parquet)
 
     df = pl.read_parquet(contribs_parquet)
-    assert set(df.columns) == set(
-        ["doi", "sunetid", "title", "first_name"]
-    ), "columns are correct"
+    assert set(df.columns) == set(["doi", "sunetid", "title", "first_name"]), (
+        "columns are correct"
+    )
 
     # first publication got joined to authors
     assert len(df.filter(pl.col("doi") == "0000/abc")) == 1

test/harvest/test_openalex.py

@@ -49,32 +49,23 @@ def test_publications_from_dois():
     # look up the publication metadata for them
     pubs = list(openalex.publications_from_dois(dois))
 
-    # >= is used because sometimes there can be multiple works for a DOI!
-    assert len(pubs) >= 231, "should paginate (page size=200)"
+    # > 200 is used because some of the 231 DOIs have been removed from openalex 🤷
+    assert len(pubs) > 200, "should paginate (page size=200)"
     assert set(openalex.FIELDS) == set(pubs[0].keys()), "All fields accounted for."
-    assert len(pubs[0].keys()) == 53, "first publication has 53 columns"
-    assert len(pubs[1].keys()) == 53, "second publication has 53 columns"
+    assert len(pubs[0].keys()) == 54, "first publication has 54 columns"
+    assert len(pubs[1].keys()) == 54, "second publication has 54 columns"
 
 
 def test_publications_from_invalid_dois(caplog):
-    # Error may change if OpenAlex API or pyalex changes
     invalid_dois = ["doi-with-comma,a", "10.1145/3442188.3445922"]
     assert len(list(openalex.publications_from_dois(invalid_dois))) == 1
-    assert (
-        "OpenAlex QueryError for doi-with-comma,a: Invalid query parameter"
-        in caplog.text
-    ), "logs error message"
 
 
 def test_publications_from_invalid_with_comma(caplog):
     # OpenAlex will interpret a DOI string with a comma as two DOIs but
     # Does not return a result for the first half even if valid. Will return an empty list
     invalid_doi = ["10.1002/cncr.33546,-(wileyonlinelibrary.com)"]
     assert len(list(openalex.publications_from_dois(invalid_doi))) == 0
-    assert (
-        "OpenAlex QueryError for 10.1002/cncr.33546,-(wileyonlinelibrary.com): Invalid query parameter"
-        in caplog.text
-    ), "logs error message"
 
 
 def test_publications_csv(tmp_path):
@@ -102,13 +93,9 @@ def test_publications_csv(tmp_path):
 
 
 def test_pyalex_urlencoding():
-    # this might start working if https://github.com/J535D165/pyalex/issues/41 is fixed
-    with pytest.raises(pyalex.api.QueryError):
-        pyalex.Works().filter(doi="10.1207/s15327809jls0703&4_2").count() == 1
-
-    assert (
-        pyalex.Works().filter(doi="10.1207/s15327809jls0703%264_2").count() == 1
-    ), "url encoding the & works with OpenAlex API"
+    assert pyalex.Works().filter(doi="10.1207/s15327809jls0703&4_2").count() == 1, (
+        "url encoding the & works with OpenAlex API"
+    )
 
     assert (
         len(
@@ -119,7 +106,7 @@ def test_pyalex_urlencoding():
             )
         )
         == 2
-    ), "we handle url URL encoding DOIs until pyalex does"
+    ), "we handle URL encoding"
 
 
 @pytest.mark.skip(reason="This record no longer exhibits the problem")