Update numpy 1.22 types and pylint (scalabel#454)

* Fix dependency versions

* Change pandas version

* Change scikit-learn  version

* Update scipy version

* Fixed linting errors in eval code

* Fixed more linting errors skipped by mypy

* Fixed incompatible type errors

* Fixed python tests

* Protobuf workaround fix

* Small fixes

* Support newest version of pylint and fix linting errors

* Remove data copy when unnecessary

Co-authored-by: cwlroda <[email protected]>
Co-authored-by: Fisher Yu <[email protected]>

.github/workflows/build.yml

@@ -14,12 +14,12 @@ jobs:
     name: lint python
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Install apt packages
         run: |
           sudo apt-get install -y libopenmpi-dev
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -49,12 +49,12 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Install apt packages
         run: |
           sudo apt-get install -y libopenmpi-dev
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -66,7 +66,9 @@ jobs:
       - name: Build
         run: python3 setup.py sdist bdist_wheel
       - name: Test
-        run: python3 -m pytest --pyargs scalabel
+        run: |
+          export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python
+          python3 -m pytest --pyargs scalabel
 
   python-mac:
     name: test py${{ matrix.python-version }} on mac
@@ -76,12 +78,12 @@ jobs:
         python-version: ["3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Install brew packages
         run: |
           brew install openmpi
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -95,6 +97,7 @@ jobs:
       - name: Test
         env:
           MPLBACKEND: TkAgg
+          PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python
         run: python3 -m pytest --pyargs scalabel
 
   nodejs:
@@ -120,9 +123,9 @@ jobs:
           - 6378:6379
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@v1
+        uses: actions/setup-node@v3
         with:
           node-version: ${{ matrix.node-version }}
       - name: Install node packages
@@ -144,7 +147,7 @@ jobs:
     name: build docker image
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
       - name: Build and export to Docker

.github/workflows/deploy-doc.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
@@ -36,4 +36,4 @@ jobs:
           AWS_S3_BUCKET: doc.scalabel.ai
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          SOURCE_DIR: "doc/_build/src/html/"
+          SOURCE_DIR: "doc/_build/src/html/"

.github/workflows/deploy-docker.yml

@@ -10,7 +10,7 @@ jobs:
     name: build and push docker image
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
       - name: Login to DockerHub

.github/workflows/setup.yml

@@ -19,7 +19,7 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # Runs a single command using the runners shell
       - name: Run setup script

.pylintrc

@@ -16,7 +16,7 @@ persistent=yes
 
 # List of plugins (as comma separated values of python modules names) to load,
 # usually to register additional checkers.
-load-plugins=pylint.extensions.docparams
+load-plugins=pylint.extensions.docparams,pylint.extensions.bad_builtin,pylint.extensions.no_self_use
 
 # Use multiple processes to speed up Pylint.
 jobs=1
@@ -40,7 +40,7 @@ confidence=
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
 # multiple time. See also the "--disable" option for examples.
-enable=use-symbolic-message-instead,useless-supression,fixme
+enable=use-symbolic-message-instead,useless-suppression,fixme
 
 # Disable the message, report, category or checker with the given id(s). You
 # can either give multiple identifiers separated by comma (,) or put this
@@ -52,10 +52,8 @@ enable=use-symbolic-message-instead,useless-supression,fixme
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
 
-# This is a bug in detecting bad continuation. Since black is handling the code
-# formatting, we can disable C0330 safely.
 # C0413: ignore wrong import order since we use isort for that
-disable=C0330, R0801, C0413
+disable=R0801, C0413
 
 
 
@@ -66,11 +64,6 @@ disable=C0330, R0801, C0413
 # mypackage.mymodule.MyReporterClass.
 output-format=text
 
-# Put messages in a separate file for each module / package specified on the
-# command line instead of printing them on stdout. Reports (if any) will be
-# written in a file name "pylint_global.[txt|html]".
-files-output=no
-
 # Tells whether to display a full report or only the messages
 reports=no
 
@@ -144,9 +137,6 @@ max-line-length=79
 # else.
 single-line-if-stmt=no
 
-# List of optional constructs for which whitespace checking is disabled
-no-space-check=trailing-comma,dict-separator
-
 # Maximum number of lines in a module
 max-module-lines=1024
 
@@ -183,61 +173,61 @@ include-naming-hint=no
 function-rgx=[a-z_][a-z0-9_]{2,30}$
 
 # Naming hint for function names
-function-name-hint=[a-z_][a-z0-9_]{2,30}$
+function-naming-style=snake_case
 
 # Regular expression matching correct variable names
 variable-rgx=[a-z_][a-z0-9_]{0,30}$
 
 # Naming hint for variable names
-variable-name-hint=[a-z_][a-z0-9_]{0,30}$
+variable-naming-style=snake_case
 
 # Regular expression matching correct constant names
 const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
 
 # Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+const-naming-style=snake_case
 
 # Regular expression matching correct attribute names
 attr-rgx=[a-z_][a-z0-9_]{1,}$
 
 # Naming hint for attribute names
-attr-name-hint=[a-z_][a-z0-9_]{1,}$
+attr-naming-style=snake_case
 
 # Regular expression matching correct argument names
 argument-rgx=[a-z_][a-z0-9_]{1,30}$
 
 # Naming hint for argument names
-argument-name-hint=[a-z_][a-z0-9_]{1,30}$
+argument-naming-style=snake_case
 
 # Regular expression matching correct class attribute names
 class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{1,30}|(__.*__))$
 
 # Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{1,30}|(__.*__))$
+class-attribute-naming-style=snake_case
 
 # Regular expression matching correct inline iteration names
 inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
 
 # Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
+inlinevar-naming-style=snake_case
 
 # Regular expression matching correct class names
 class-rgx=[A-Z_][a-zA-Z0-9]+$
 
 # Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
+class-naming-style=snake_case
 
 # Regular expression matching correct module names
 module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
 # Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+module-naming-style=snake_case
 
 # Regular expression matching correct method names
 method-rgx=[a-z_][a-z0-9_]{2,}$
 
 # Naming hint for method names
-method-name-hint=[a-z_][a-z0-9_]{2,}$
+method-naming-style=snake_case
 
 # Regular expression which should only match function or class names that do
 # not require a docstring.
@@ -369,4 +359,4 @@ int-import-graph=
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=Exception

scalabel/bot/polyrnn_adapter.py

@@ -4,7 +4,7 @@
 from typing import Dict, List
 
 import numpy as np
-from Tool.tool import Tool  # pylint: disable=import-error
+from Tool.tool import Tool
 
 from ..common.typing import NDArrayF64, NDArrayU8
 from .seg_base import SegBase

scalabel/eval/boundary.py

@@ -75,7 +75,6 @@ class BoundaryResult(Result):
     F1_pix2: List[Dict[str, float]]
     F1_pix5: List[Dict[str, float]]
 
-    # pylint: disable=useless-super-delegation
     def __eq__(self, other: "BoundaryResult") -> bool:  # type: ignore
         """Check whether two instances are equal."""
         return super().__eq__(other)
@@ -142,7 +141,7 @@ def eval_bdry_per_frame(
 ) -> Dict[str, NDArrayF64]:
     """Compute mean, recall, and decay from per-frame evaluation."""
     w, h = image_size.width, image_size.height
-    blank_mask = np.zeros((h, w))
+    blank_mask: NDArrayU8 = np.zeros((h, w), dtype=np.uint8)
     task2arr: Dict[str, NDArrayF64] = {}  # str -> 2d array
     if gt_frame.labels is None:
         gt_frame.labels = []
@@ -157,18 +156,16 @@ def eval_bdry_per_frame(
     for task_name, cats in categories.items():
         task_scores: List[List[float]] = []
         for cat in cats:
-            gt_mask = (
+            gt_mask: NDArrayU8 = (
                 rle_to_mask(gt_masks[cat.name])
                 if cat.name in gt_masks
                 else blank_mask
             )
-            gt_mask = gt_mask > 0
-            pd_mask = (
+            pd_mask: NDArrayU8 = (
                 rle_to_mask(pd_masks[cat.name])
                 if cat.name in pd_masks
                 else blank_mask
             )
-            pd_mask = pd_mask > 0
             cat_scores = [
                 eval_bdry_per_thr(
                     gt_mask,

scalabel/eval/detect.py

@@ -210,7 +210,7 @@ def evaluate(self) -> None:
                     self.compute_match, range(len(p.imgIds))
                 )
         else:
-            to_updates = list(map(self.compute_match, range(len(p.imgIds))))
+            to_updates = [self.compute_match(i) for i in range(len(p.imgIds))]
 
         eval_num = len(p.catIds) * len(p.areaRng) * len(p.imgIds)
         self.evalImgs: List[DictStrAny] = [{} for _ in range(eval_num)]

scalabel/eval/mot.py

@@ -158,7 +158,7 @@ def get_frame_index(frame: Frame) -> int:
                 )
             if gt_ignores.shape[0] > 0:
                 # 1. assign gt and preds
-                fps: NDArrayU8 = np.ones(pred_bboxes_c.shape[0]).astype(bool)
+                fps: NDArrayU8 = np.ones(pred_bboxes_c.shape[0], dtype=bool)
                 le, ri = mm.lap.linear_sum_assignment(distances)
                 for m, n in zip(le, ri):
                     if np.isfinite(distances[m, n]):

scalabel/eval/mots.py

@@ -111,7 +111,7 @@ def get_frame_index(frame: Frame) -> int:
                 )
             if len(gt_ignores) > 0 and len(pred_rles_c) > 0:
                 # 1. assign gt and preds
-                fps: NDArrayU8 = np.ones(len(pred_rles_c)).astype(bool)
+                fps: NDArrayU8 = np.ones(len(pred_rles_c), dtype=bool)
                 le, ri = mm.lap.linear_sum_assignment(distances)
                 for m, n in zip(le, ri):
                     if np.isfinite(distances[m, n]):

scalabel/eval/pan_seg.py

@@ -64,7 +64,6 @@ class PanSegResult(Result):
     RQ: List[Dict[str, float]]
     NUM: List[Dict[str, int]]
 
-    # pylint: disable=useless-super-delegation
     def __eq__(self, other: "PanSegResult") -> bool:  # type: ignore
         """Check whether two instances are equal."""
         return super().__eq__(other)

scalabel/eval/pose.py

@@ -157,7 +157,7 @@ def evaluate(self) -> None:
                     self.compute_match, range(len(p.imgIds))
                 )
         else:
-            to_updates = list(map(self.compute_match, range(len(p.imgIds))))
+            to_updates = [self.compute_match(i) for i in range(len(p.imgIds))]
 
         eval_num = len(p.catIds) * len(p.areaRng) * len(p.imgIds)
         self.evalImgs: List[DictStrAny] = [{} for _ in range(eval_num)]

scalabel/eval/result.py

@@ -131,7 +131,7 @@ def table(
             strs.insert(row_ind, split_line)
         summary = "".join([f"{s}\n" for s in strs])
         summary = "\n" + summary
-        return summary  # type: ignore
+        return str(summary)
 
     def __str__(self) -> str:
         """Convert the data into a printable string."""