Update pre-commit dependencies (#353)

* Update pre-commit dependencies

* Fix `flake8` errors (two typos in var names)

* Fix `mypy` importing errors

* Fix `mypy` code errors

* Update `conda/dev.yml`

.pre-commit-config.yaml

@@ -4,35 +4,41 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
         exclude: conda/meta.yaml
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
   # https://github.com/pre-commit/pre-commit/issues/1206
   - repo: https://github.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 7.1.1
     hooks:
       - id: flake8
         args: ["--config=setup.cfg"]
         additional_dependencies: [flake8-isort]
         exclude: analysis_data_preprocess
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.790
+    rev: v1.11.2
     hooks:
       - id: mypy
-        args: ["--config=setup.cfg"]
+        args: ["--config=setup.cfg", "--install-types", "--non-interactive"]
+        exclude: test*
+
+# https://pre-commit.ci/#configuration
+ci:
+  autofix_prs: false
+  autoupdate_schedule: monthly

conda/dev.yml

@@ -13,11 +13,11 @@ dependencies:
   # Developer Tools
   # =================
   # If versions are updated, also update 'rev' in `.pre-commit.config.yaml`
-  - black=22.8.0
-  - flake8=5.0.4
-  - flake8-isort=4.2.0
-  - mypy=0.982
-  - pre-commit=2.20.0
+  - black=24.10.0
+  - flake8=7.1.1
+  - flake8-isort=6.1.1
+  - mypy=1.11.2
+  - pre-commit=4.0.1
   - tbump=6.9.0
   # Documentation
   # =================

zstash/create.py

@@ -24,7 +24,6 @@
 
 def create():
     cache: str
-    exclude: str
     cache, args = setup_create()
 
     # Check config fields

zstash/extract.py

@@ -254,7 +254,7 @@ def extract_database(
     # This is because we may have different versions of the
     # same file across many tars.
     insert_idx: int
-    iter_inx: int
+    iter_idx: int
     insert_idx, iter_idx = 0, 1
     for iter_idx in range(1, len(matches)):
         # If the filenames are unique, just increment insert_idx.
@@ -351,10 +351,10 @@ def multiprocess_extract(
     for db_row in matches:
         tar = db_row.tar
         workers_idx: int
-        for worker_idx in range(len(workers_to_tars)):
-            if tar in workers_to_tars[worker_idx]:
+        for workers_idx in range(len(workers_to_tars)):
+            if tar in workers_to_tars[workers_idx]:
                 # This worker gets this db_row.
-                workers_to_matches[worker_idx].append(db_row)
+                workers_to_matches[workers_idx].append(db_row)
 
     tar_ordering: List[str] = sorted([tar for tar in tar_to_size])
     monitor: parallel.PrintMonitor = parallel.PrintMonitor(tar_ordering)
@@ -444,8 +444,7 @@ def extractFiles(  # noqa: C901
     if multiprocess_worker:
         # All messages to the logger will now be sent to
         # this queue, instead of sys.stdout.
-        # error: Argument 1 to "StreamHandler" has incompatible type "PrintQueue"; expected "Optional[IO[str]]"
-        sh = logging.StreamHandler(multiprocess_worker.print_queue)  # type: ignore
+        sh = logging.StreamHandler(multiprocess_worker.print_queue)
         sh.setLevel(logging.DEBUG)
         formatter: logging.Formatter = logging.Formatter("%(levelname)s: %(message)s")
         sh.setFormatter(formatter)
@@ -539,8 +538,7 @@ def extractFiles(  # noqa: C901
                 # error: Name 'tarfile.ExFileObject' is not defined
                 extracted_file: Optional[tarfile.ExFileObject] = tar.extractfile(tarinfo)  # type: ignore
                 if extracted_file:
-                    # error: Name 'tarfile.ExFileObject' is not defined
-                    fin: tarfile.ExFileObject = extracted_file  # type: ignore
+                    fin: tarfile.ExFileObject = extracted_file
                 else:
                     raise TypeError("Invalid extracted_file={}".format(extracted_file))
                 try:

zstash/hpss_utils.py

@@ -176,8 +176,7 @@ def add_file(
     tar: tarfile.TarFile, file_name: str, follow_symlinks: bool
 ) -> Tuple[int, int, datetime, Optional[str]]:
 
-    # FIXME: error: "TarFile" has no attribute "offset"
-    offset: int = tar.offset  # type: ignore
+    offset: int = tar.offset
     tarinfo: tarfile.TarInfo = tar.gettarinfo(file_name)
     # Change the size of any hardlinks from 0 to the size of the actual file
     if tarinfo.islnk():
@@ -215,8 +214,7 @@ def add_file(
                     fileobj.write(null_bytes * (tarfile.BLOCKSIZE - remainder))
                     blocks += 1
                 # Increase the offset by the amount already saved to the tar
-                # FIXME: error: "TarFile" has no attribute "offset"
-                tar.offset += blocks * tarfile.BLOCKSIZE  # type: ignore
+                tar.offset += blocks * tarfile.BLOCKSIZE
                 break
         f.close()
         md5 = hash_md5.hexdigest()