Merge branch 'master' into datecreatedbyapplication

.pre-commit-config.yaml

@@ -1,28 +1,12 @@
 repos:
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.1
   hooks:
-  - id: pyupgrade
-    args: [--py38-plus]
-- repo: https://github.com/asottile/reorder_python_imports
-  rev: v3.12.0
-  hooks:
-  - id: reorder-python-imports
-    args: [--py38-plus]
-- repo: https://github.com/psf/black
-  rev: "23.11.0"
-  hooks:
-  - id: black
-    args: [--safe, --quiet]
-- repo: https://github.com/pycqa/flake8
-  rev: "6.1.0"
-  hooks:
-  - id: flake8
-    additional_dependencies:
-    - flake8-bugbear==23.9.16
-    - flake8-comprehensions==3.14.0
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+  - id: ruff-format
 - repo: https://github.com/igorshubovych/markdownlint-cli
-  rev: v0.37.0
+  rev: v0.41.0
   hooks:
   - id: markdownlint
     exclude: |

README.md

@@ -286,7 +286,7 @@ corner, then select 'Your profile'. The API key will be displayed at the bottom
 of the page.
 
 To get the Storage Service API key, log in to the Storage Service as the user
-you wish to authenticate as. From the dashboard, go to *Administration > Users*
+you wish to authenticate as. From the dashboard, go to _Administration > Users_
 and select 'Edit' for the user you want the key for. The API key will be
 displayed at the bottom of the page. Storage Service versions earlier than
 `0.8.x` do not require an API key, and will not provide one. In that case, fill
@@ -825,7 +825,7 @@ above about finding the Archivematica and Storage Service API keys. An example
 configuration with placeholder parameters is provided in
 [reingestconfig.json](transfers/reingestconfig.json)
 
-*Reingest.py* is best used via the shell script provided in the
+_Reingest.py_ is best used via the shell script provided in the
 [_transfers/examples/reingest_](transfers/examples/reingest) folder. As it is
 designed for bulk-reingest, it is best used in conjunction with a cronfile, an
 example of which is provided in the same folder.
@@ -883,7 +883,7 @@ INFO      2018-10-26 00:00:03 reingest.py:194  Removing PID for current process.
 ```
 
 1. Following completion of the first reingest, a second is started and we can
-   see similar log entries to those in *1.*
+   see similar log entries to those in _1._
 
 ```shell
 $ ./run-reingest.sh
@@ -935,13 +935,13 @@ information could be found by looking up the status of the microservices:
 
 Via the user interface:
 
-- *http://{archivematica-url}}/transfer/{UUID}/*
-- *http://{archivematica-url}}/ingest/{UUID}/*
+- _http://{archivematica-url}}/transfer/{UUID}/_
+- _http://{archivematica-url}}/ingest/{UUID}/_
 
 Via the API (users will need to filter on package UUID):
 
-- *http://{archivematica-url}}/transfer/status/*
-- *http://{archivematica-url}}/ingest/status/*
+- _http://{archivematica-url}}/transfer/status/_
+- _http://{archivematica-url}}/ingest/status/_
 
 ## Related Projects
 

aips/create_dip.py

@@ -11,6 +11,7 @@
 generated alongside the objects folder containing only a reference to the ZIP file
 (without AMD or DMD sections).
 """
+
 import argparse
 import csv
 import logging.config  # Has to be imported separately

aips/create_dips_job.py

@@ -9,6 +9,7 @@
 Optionally, uploads those DIPs to AtoM or the Storage Service using
 the scripts from `dips` and deletes the local copy.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os

aips/models.py

@@ -1,10 +1,10 @@
 from os.path import isfile
 
 from sqlalchemy import Column
-from sqlalchemy import create_engine
 from sqlalchemy import Integer
 from sqlalchemy import Sequence
 from sqlalchemy import String
+from sqlalchemy import create_engine
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
 

dips/atom_upload.py

@@ -6,6 +6,7 @@
 AtoM instance. A passwordless SSH connection is required to the AtoM host for the
 user running this script and it must be already added to the list of known hosts.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os
@@ -15,7 +16,6 @@
 
 import requests
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("dip_workflow")
 

dips/copy_to_netx.py

@@ -4,6 +4,7 @@
 
 Copies a local DIP to NetX, providing a CSV list of each object.
 """
+
 import argparse
 import csv
 import logging.config  # Has to be imported separately
@@ -14,7 +15,6 @@
 
 import lxml.etree
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("copy_to_netx")
 

dips/storage_service_upload.py

@@ -8,6 +8,7 @@
 Storage Service to process that DIP and create a relationship with the
 AIP from where it was created.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os
@@ -17,7 +18,6 @@
 
 import requests
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("dip_workflow")
 

requirements-dev.in

@@ -1,3 +1,4 @@
 -r requirements.txt
 pytest
 pytest-cov
+ruff

requirements-dev.txt

@@ -6,55 +6,57 @@
 #
 amclient==1.3.0
     # via -r requirements.txt
-certifi==2023.11.17
+certifi==2024.7.4
     # via
     #   -r requirements.txt
     #   requests
 charset-normalizer==3.3.2
     # via
     #   -r requirements.txt
     #   requests
-coverage[toml]==7.3.2
+coverage[toml]==7.5.4
     # via pytest-cov
-exceptiongroup==1.2.0
+exceptiongroup==1.2.1
     # via pytest
-greenlet==3.0.1
+greenlet==3.0.3
     # via
     #   -r requirements.txt
     #   sqlalchemy
-idna==3.4
+idna==3.7
     # via
     #   -r requirements.txt
     #   requests
 iniconfig==2.0.0
     # via pytest
-lxml==4.9.3
+lxml==5.2.2
     # via
     #   -r requirements.txt
     #   metsrw
-metsrw==0.5.0
+metsrw==0.5.1
     # via -r requirements.txt
-packaging==23.2
+packaging==24.1
     # via pytest
-pluggy==1.3.0
+pluggy==1.5.0
     # via pytest
-pytest==7.4.3
+pytest==8.2.2
     # via
     #   -r requirements-dev.in
     #   pytest-cov
-pytest-cov==4.1.0
+pytest-cov==5.0.0
     # via -r requirements-dev.in
-requests==2.31.0
+requests==2.32.3
     # via
     #   -r requirements.txt
     #   amclient
-sqlalchemy==1.4.50
+ruff==0.5.1
+    # via -r requirements-dev.in
+sqlalchemy==1.4.52
     # via -r requirements.txt
 tomli==2.0.1
     # via
     #   coverage
     #   pytest
-urllib3==2.1.0
+urllib3==2.2.2
     # via
     #   -r requirements.txt
     #   amclient

requirements.txt

@@ -6,25 +6,25 @@
 #
 amclient==1.3.0
     # via -r requirements.in
-certifi==2023.11.17
+certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
     # via requests
-greenlet==3.0.1
+greenlet==3.0.3
     # via sqlalchemy
-idna==3.4
+idna==3.7
     # via requests
-lxml==4.9.3
+lxml==5.2.2
     # via metsrw
-metsrw==0.5.0
+metsrw==0.5.1
     # via -r requirements.in
-requests==2.31.0
+requests==2.32.3
     # via
     #   -r requirements.in
     #   amclient
-sqlalchemy==1.4.50
+sqlalchemy==1.4.52
     # via -r requirements.in
-urllib3==2.1.0
+urllib3==2.2.2
     # via
     #   -r requirements.in
     #   amclient

ruff.toml

@@ -0,0 +1,19 @@
+[lint]
+# Rule reference: https://docs.astral.sh/ruff/rules/
+select = [
+  "B",
+  "C4",
+  "E",
+  "F",
+  "I",
+  "UP",
+  "W",
+]
+ignore = [
+  "B904",
+  "E501",
+  "UP031",
+]
+
+[lint.isort]
+force-single-line = true

tests/test_create_avalon_dip.py

@@ -9,7 +9,6 @@
 
 from aips import create_dip
 
-
 SS_URL = "http://127.0.0.1:62081"
 SS_USER_NAME = "test"
 SS_API_KEY = "test"
@@ -68,8 +67,8 @@ def test_create_avalon_dip_success(_get, tmp_path):
         aip_dir, AVALON_AIP_UUID, output_dir.as_posix(), "atom", "avalon-manifest"
     )
     # Check DIP structure
-    assert avalon_dip_dir == "{}/{}/{}".format(
-        output_dir.as_posix(), TRANSFER_NAME, AVALON_AIP_UUID
+    assert (
+        avalon_dip_dir == f"{output_dir.as_posix()}/{TRANSFER_NAME}/{AVALON_AIP_UUID}"
     )
     assert os.path.isdir(avalon_dip_dir)
 

tests/test_create_dip.py

@@ -10,7 +10,6 @@
 
 from aips import create_dip
 
-
 SS_URL = "http://192.168.168.192:8000"
 SS_USER_NAME = "test"
 SS_API_KEY = "7021334bee4c9155c07e531608dd28a9d8039420"