Merge pull request #2 from HakaiInstitute/update-deps

Update dependencies, switch to Python 3.11

.github/workflows/gui-release.yml

@@ -20,15 +20,15 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
 
       - name: Setup Poetry
-        uses: abatilo/actions-poetry@v2.0.0
+        uses: abatilo/actions-poetry@v2.3.0
         with:
           poetry-version: 1.2.2
 
@@ -38,13 +38,13 @@ jobs:
       - name: Install Linux dependencies
         if: ${{ runner.os == 'Linux' }}
         run: >
-          sudo apt-get install 
-          '^libxcb.*-dev' 
-          libx11-xcb-dev 
-          libglu1-mesa-dev 
-          libxrender-dev 
-          libxi-dev 
-          libxkbcommon-dev 
+          sudo apt-get install
+          '^libxcb.*-dev'
+          libx11-xcb-dev
+          libglu1-mesa-dev
+          libxrender-dev
+          libxi-dev
+          libxkbcommon-dev
           libxkbcommon-x11-dev
 
       - name: Install dependencies
@@ -86,7 +86,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Get tag
         id: tag

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+  - repo: https://github.com/python-poetry/poetry
+    rev:  1.4.0
+    hooks:
+      - id: poetry-check
+      - id: poetry-lock
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.265
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black

las_trx/__main__.py

@@ -27,7 +27,7 @@
     sync_missing_grid_files,
     utm_zone_to_coord_type,
     resource_path,
-    get_upgrade_version
+    get_upgrade_version,
 )
 from las_trx.worker import TransformWorker
 
@@ -50,7 +50,8 @@ def __init__(self):
             self.label_upgrade_link.setText(
                 f"<a href=\"{upgrade_version['html_url']}\">"
                 f"New version available (v{upgrade_version['tag_name']})"
-                f"</a>")
+                f"</a>"
+            )
 
         self.done_msg_box = QMessageBox(self)
         self.done_msg_box.setText("File(s) converted successfully")
@@ -287,15 +288,15 @@ def run(self):
     window = MainWindow()
 
     if os.getenv("DEBUG"):
-        # self.lineEdit_input_file.setText(
-        #     "/mnt/aco-uvic/2020_Acquisitions/02_processed/20_3028_01_FraserRiver_ChimmneyCreek_WestWilliams_Canyon/01_LiDAR/01_Deliverables/02_QC/02_Classified_tiles/546000_5768000_5m_stp_arch_grnd_denoised.laz")
         window.lineEdit_input_file.setText(
-            "/home/taylor/PycharmProjects/Las-TRX/testfiles/20_3028_01/*.laz")
+            "/home/taylor/PycharmProjects/Las-TRX/testfiles/20_3028_01/*.laz"
+        )
         window.comboBox_input_reference.setCurrentText("ITRF2014")
         window.dateEdit_input_epoch.setDate(date(2020, 8, 12))
 
         window.lineEdit_output_file.setText(
-            "/home/taylor/PycharmProjects/Las-TRX/testfiles/20_3028_01_converted/{}.laz")
+            "/home/taylor/PycharmProjects/Las-TRX/testfiles/20_3028_01_converted/{}.laz"
+        )
         window.checkBox_epoch_trans.setChecked(True)
         window.dateEdit_output_epoch.setEnabled(True)
         window.dateEdit_output_epoch.setDate(date(2002, 1, 1))

las_trx/config.py

@@ -1,7 +1,7 @@
 from datetime import date
 from typing import Union
 
-from pydantic import BaseModel, validator
+from pydantic import BaseModel, field_validator, FieldValidationInfo
 from pyproj.crs import (
     CRS,
     CompoundCRS,
@@ -27,9 +27,17 @@ class TransformConfig(BaseModel):
     s_coords: Union[enums.CoordType, str]
     t_coords: Union[enums.CoordType, str]
 
-    # validators
-    _normalize_s_epoch = validator("s_epoch", allow_reuse=True)(date_to_decimal_year)
-    _normalize_t_epoch = validator("t_epoch", allow_reuse=True)(date_to_decimal_year)
+    @classmethod
+    @field_validator("s_epoch", "t_epoch")
+    def check_decimal_date(
+        cls, v: Union[float, date], info: FieldValidationInfo
+    ) -> float:
+        if isinstance(v, float):
+            return v
+        elif isinstance(v, date):
+            return date_to_decimal_year(v)
+        else:
+            raise TypeError(f"Invalid type for {info.field_name}: {type(v)}")
 
     @property
     def t_crs(self) -> CRS:

las_trx/utils.py

@@ -18,9 +18,7 @@ def date_to_decimal_year(d: date) -> float:
     ...
 
 
-def date_to_decimal_year(d: T) -> T:
-    if not isinstance(d, date):
-        return d
+def date_to_decimal_year(d: date) -> float:
     year_part = d - date(d.year, 1, 1)
     year_length = date(d.year + 1, 1, 1) - date(d.year, 1, 1)
     return d.year + year_part / year_length
@@ -138,12 +136,14 @@ def resource_path(relative_path):
 
 def _get_available_versions() -> Optional[List[Mapping[str, Any]]]:
     import requests
+
     headers = {
         "Accept": "application/vnd.github+json",
-        "X-GitHub-Api-Version": "2022-11-28"
+        "X-GitHub-Api-Version": "2022-11-28",
     }
-    r = requests.get("https://api.github.com/repos/HakaiInstitute/LAS-TRX/releases",
-                     headers=headers)
+    r = requests.get(
+        "https://api.github.com/repos/HakaiInstitute/LAS-TRX/releases", headers=headers
+    )
     if r.status_code == requests.codes.ok:
         return list(
             {
@@ -172,8 +172,9 @@ def get_upgrade_version(version) -> Optional[Mapping[str, str]]:
         idx = len(available_versions)
 
     # Only recommend stable releases for upgrade
-    newer_stable_versions = [v for v in available_versions[:idx] if
-                             not v["prerelease"] and not v["draft"]]
+    newer_stable_versions = [
+        v for v in available_versions[:idx] if not v["prerelease"] and not v["draft"]
+    ]
 
     if len(newer_stable_versions) == 0:
         return None

las_trx/worker.py

@@ -29,8 +29,9 @@ class TransformWorker(QThread):
     success = Signal()
     error = Signal(BaseException)
 
-    def __init__(self, config: TransformConfig, input_files: list[Path],
-                 output_files: list[Path]):
+    def __init__(
+        self, config: TransformConfig, input_files: list[Path], output_files: list[Path]
+    ):
         super().__init__(parent=None)
         self.config = config
         self.input_files = input_files
@@ -119,11 +120,11 @@ def run(self):
 
 
 def transform(
-        config: dict,
-        input_file: Path,
-        output_file: Path,
-        lock: multiprocessing.RLock,
-        cur: multiprocessing.Value,
+    config: dict,
+    input_file: Path,
+    output_file: Path,
+    lock: multiprocessing.RLock,
+    cur: multiprocessing.Value,
 ):
     transformer = CSRSTransformer(**config)
     config = TransformConfig(**config)
@@ -139,7 +140,7 @@ def transform(
         logger.debug(f"{laz_backend=}")
 
         with laspy.open(
-                str(output_file), mode="w", header=new_header, laz_backend=laz_backend
+            str(output_file), mode="w", header=new_header, laz_backend=laz_backend
         ) as out_las:
             for points in in_las.chunk_iterator(CHUNK_SIZE):
                 # Convert the coordinates
@@ -160,7 +161,7 @@ def transform(
 
 
 def write_header_offsets(
-        header: "LasHeader", input_file: Path, transformer: "CSRSTransformer"
+    header: "LasHeader", input_file: Path, transformer: "CSRSTransformer"
 ) -> "LasHeader":
     with laspy.open(str(input_file)) as in_las:
         points = next(in_las.chunk_iterator(CHUNK_SIZE))
@@ -179,10 +180,10 @@ def clear_header_geokeys(header: "LasHeader") -> "LasHeader":
     # Update GeoKeyDirectoryVLR
     # check and remove any existing crs vlrs
     for crs_vlr_name in (
-            "WktCoordinateSystemVlr",
-            "GeoKeyDirectoryVlr",
-            "GeoAsciiParamsVlr",
-            "GeoDoubleParamsVlr",
+        "WktCoordinateSystemVlr",
+        "GeoKeyDirectoryVlr",
+        "GeoAsciiParamsVlr",
+        "GeoDoubleParamsVlr",
     ):
         try:
             header.vlrs.extract(crs_vlr_name)