Fix incorrect test import and clarify backend test dependencies

package/error_log.txt

@@ -0,0 +1,75 @@
+Obtaining file:///C:/Users/Lenovo/Method-section-generator/package
+  Installing build dependencies: started
+  Installing build dependencies: finished with status 'done'
+  Checking if build backend supports build_editable: started
+  Checking if build backend supports build_editable: finished with status 'done'
+  Getting requirements to build editable: started
+  Getting requirements to build editable: finished with status 'done'
+  Preparing editable metadata (pyproject.toml): started
+  Preparing editable metadata (pyproject.toml): finished with status 'done'
+Collecting PyYAML~=6.0.2 (from pyaslreport==0.0.3)
+  Obtaining dependency information for PyYAML~=6.0.2 from https://files.pythonhosted.org/packages/74/93/7baea19427dcfbe1e5a372d81473250b379f04b1bd3c4c5ff825e2327202/pyyaml-6.0.3-cp312-cp312-win32.whl.metadata
+  Using cached pyyaml-6.0.3-cp312-cp312-win32.whl.metadata (2.4 kB)
+Collecting numpy~=2.2.6 (from pyaslreport==0.0.3)
+  Obtaining dependency information for numpy~=2.2.6 from https://files.pythonhosted.org/packages/57/0a/72d5a3527c5ebffcd47bde9162c39fae1f90138c961e5296491ce778e682/numpy-2.2.6-cp312-cp312-win32.whl.metadata
+  Using cached numpy-2.2.6-cp312-cp312-win32.whl.metadata (60 kB)
+Collecting nibabel~=5.3.2 (from pyaslreport==0.0.3)
+  Obtaining dependency information for nibabel~=5.3.2 from https://files.pythonhosted.org/packages/b8/f5/7f6aa3bbff013c0bf993129cbb2b1505790091f812accbe85cf001514737/nibabel-5.3.3-py3-none-any.whl.metadata
+  Using cached nibabel-5.3.3-py3-none-any.whl.metadata (9.1 kB)
+Collecting pydicom~=3.0.1 (from pyaslreport==0.0.3)
+  Obtaining dependency information for pydicom~=3.0.1 from https://files.pythonhosted.org/packages/27/a6/98651e752a49f341aa99aa3f6c8ba361728dfc064242884355419df63669/pydicom-3.0.1-py3-none-any.whl.metadata
+  Using cached pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)
+Collecting dicom2nifti~=2.6.2 (from pyaslreport==0.0.3)
+  Obtaining dependency information for dicom2nifti~=2.6.2 from https://files.pythonhosted.org/packages/ab/59/598237cb4a5b1fae3515ad8b402ae815a5551e236e530ba11b7a17b2c036/dicom2nifti-2.6.2-py3-none-any.whl.metadata
+  Using cached dicom2nifti-2.6.2-py3-none-any.whl.metadata (1.5 kB)
+Collecting scipy (from dicom2nifti~=2.6.2->pyaslreport==0.0.3)
+  Using cached scipy-1.17.1.tar.gz (30.6 MB)
+  Installing build dependencies: started
+  Installing build dependencies: finished with status 'done'
+  Getting requirements to build wheel: started
+  Getting requirements to build wheel: finished with status 'done'
+  Installing backend dependencies: started
+  Installing backend dependencies: finished with status 'done'
+  Preparing metadata (pyproject.toml): started
+  Preparing metadata (pyproject.toml): finished with status 'error'
+  error: subprocess-exited-with-error
+
+  Preparing metadata (pyproject.toml) did not run successfully.
+  exit code: 1
+
+  [21 lines of output]
+  + meson setup C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30 C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30\.mesonpy-36syoiyu -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30\.mesonpy-36syoiyu\meson-python-native-file.ini
+  The Meson build system
+  Version: 1.10.1
+  Source dir: C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30
+  Build dir: C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30\.mesonpy-36syoiyu
+  Build type: native build
+  WARNING: Failed to activate VS environment: Could not find C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe
+  Project name: scipy
+  Project version: 1.17.1
+
+  ..\meson.build:1:0: ERROR: Unknown compiler(s): [['icl'], ['cl'], ['cc'], ['gcc'], ['clang'], ['clang-cl'], ['pgcc']]
+  The following exception(s) were encountered:
+  Running `icl ""` gave "[WinError 2] The system cannot find the file specified"
+  Running `cl /?` gave "[WinError 2] The system cannot find the file specified"
+  Running `cc --version` gave "[WinError 2] The system cannot find the file specified"
+  Running `gcc --version` gave "[WinError 2] The system cannot find the file specified"
+  Running `clang --version` gave "[WinError 2] The system cannot find the file specified"
+  Running `clang-cl /?` gave "[WinError 2] The system cannot find the file specified"
+  Running `pgcc --version` gave "[WinError 2] The system cannot find the file specified"
+
+  A full log can be found at C:\Users\Lenovo\AppData\Local\Temp\pip-install-pdslx5nq\scipy_37e282a689d44d52a49fdbc0e67acf30\.mesonpy-36syoiyu\meson-logs\meson-log.txt
+  [end of output]
+
+  note: This error originates from a subprocess, and is likely not a problem with pip.
+error: metadata-generation-failed
+
+Encountered error while generating package metadata.
+
+See above for output.
+
+note: This is an issue with the package mentioned above, not pip.
+hint: See above for details.
+
+[notice] A new release of pip is available: 23.2.1 -> 26.0.1
+[notice] To update, run: python.exe -m pip install --upgrade pip

package/src/pyaslreport/tests/test_package.py

@@ -1,6 +1,6 @@
 import pytest
 from unittest.mock import patch, MagicMock
-from .main import get_bids_metadata
+from pyaslreport.main import get_bids_metadata
 
 # filepath: /home/ibrahim/MyPc/Projects/GSoC/ASL-Parameter-Generator/package/src/pyaslreport/test_main.py
 

tests/test_basic.py

@@ -0,0 +1,2 @@
+def test_basic_math():
+    assert 1 + 1 == 2

venv/Lib/site-packages/PIL/AvifImagePlugin.py

@@ -0,0 +1,293 @@
+from __future__ import annotations
+
+import os
+from io import BytesIO
+from typing import IO
+
+from . import ExifTags, Image, ImageFile
+
+try:
+    from . import _avif
+
+    SUPPORTED = True
+except ImportError:
+    SUPPORTED = False
+
+# Decoder options as module globals, until there is a way to pass parameters
+# to Image.open (see https://github.com/python-pillow/Pillow/issues/569)
+DECODE_CODEC_CHOICE = "auto"
+DEFAULT_MAX_THREADS = 0
+
+
+def get_codec_version(codec_name: str) -> str | None:
+    versions = _avif.codec_versions()
+    for version in versions.split(", "):
+        if version.split(" [")[0] == codec_name:
+            return version.split(":")[-1].split(" ")[0]
+    return None
+
+
+def _accept(prefix: bytes) -> bool | str:
+    if prefix[4:8] != b"ftyp":
+        return False
+    major_brand = prefix[8:12]
+    if major_brand in (
+        # coding brands
+        b"avif",
+        b"avis",
+        # We accept files with AVIF container brands; we can't yet know if
+        # the ftyp box has the correct compatible brands, but if it doesn't
+        # then the plugin will raise a SyntaxError which Pillow will catch
+        # before moving on to the next plugin that accepts the file.
+        #
+        # Also, because this file might not actually be an AVIF file, we
+        # don't raise an error if AVIF support isn't properly compiled.
+        b"mif1",
+        b"msf1",
+    ):
+        if not SUPPORTED:
+            return (
+                "image file could not be identified because AVIF support not installed"
+            )
+        return True
+    return False
+
+
+def _get_default_max_threads() -> int:
+    if DEFAULT_MAX_THREADS:
+        return DEFAULT_MAX_THREADS
+    if hasattr(os, "sched_getaffinity"):
+        return len(os.sched_getaffinity(0))
+    else:
+        return os.cpu_count() or 1
+
+
+class AvifImageFile(ImageFile.ImageFile):
+    format = "AVIF"
+    format_description = "AVIF image"
+    __frame = -1
+
+    def _open(self) -> None:
+        if not SUPPORTED:
+            msg = "image file could not be opened because AVIF support not installed"
+            raise SyntaxError(msg)
+
+        if DECODE_CODEC_CHOICE != "auto" and not _avif.decoder_codec_available(
+            DECODE_CODEC_CHOICE
+        ):
+            msg = "Invalid opening codec"
+            raise ValueError(msg)
+
+        assert self.fp is not None
+        self._decoder = _avif.AvifDecoder(
+            self.fp.read(),
+            DECODE_CODEC_CHOICE,
+            _get_default_max_threads(),
+        )
+
+        # Get info from decoder
+        self._size, self.n_frames, self._mode, icc, exif, exif_orientation, xmp = (
+            self._decoder.get_info()
+        )
+        self.is_animated = self.n_frames > 1
+
+        if icc:
+            self.info["icc_profile"] = icc
+        if xmp:
+            self.info["xmp"] = xmp
+
+        if exif_orientation != 1 or exif:
+            exif_data = Image.Exif()
+            if exif:
+                exif_data.load(exif)
+                original_orientation = exif_data.get(ExifTags.Base.Orientation, 1)
+            else:
+                original_orientation = 1
+            if exif_orientation != original_orientation:
+                exif_data[ExifTags.Base.Orientation] = exif_orientation
+                exif = exif_data.tobytes()
+        if exif:
+            self.info["exif"] = exif
+        self.seek(0)
+
+    def seek(self, frame: int) -> None:
+        if not self._seek_check(frame):
+            return
+
+        # Set tile
+        self.__frame = frame
+        self.tile = [ImageFile._Tile("raw", (0, 0) + self.size, 0, self.mode)]
+
+    def load(self) -> Image.core.PixelAccess | None:
+        if self.tile:
+            # We need to load the image data for this frame
+            data, timescale, pts_in_timescales, duration_in_timescales = (
+                self._decoder.get_frame(self.__frame)
+            )
+            self.info["timestamp"] = round(1000 * (pts_in_timescales / timescale))
+            self.info["duration"] = round(1000 * (duration_in_timescales / timescale))
+
+            if self.fp and self._exclusive_fp:
+                self.fp.close()
+            self.fp = BytesIO(data)
+
+        return super().load()
+
+    def load_seek(self, pos: int) -> None:
+        pass
+
+    def tell(self) -> int:
+        return self.__frame
+
+
+def _save_all(im: Image.Image, fp: IO[bytes], filename: str | bytes) -> None:
+    _save(im, fp, filename, save_all=True)
+
+
+def _save(
+    im: Image.Image, fp: IO[bytes], filename: str | bytes, save_all: bool = False
+) -> None:
+    info = im.encoderinfo.copy()
+    if save_all:
+        append_images = list(info.get("append_images", []))
+    else:
+        append_images = []
+
+    total = 0
+    for ims in [im] + append_images:
+        total += getattr(ims, "n_frames", 1)
+
+    quality = info.get("quality", 75)
+    if not isinstance(quality, int) or quality < 0 or quality > 100:
+        msg = "Invalid quality setting"
+        raise ValueError(msg)
+
+    duration = info.get("duration", 0)
+    subsampling = info.get("subsampling", "4:2:0")
+    speed = info.get("speed", 6)
+    max_threads = info.get("max_threads", _get_default_max_threads())
+    codec = info.get("codec", "auto")
+    if codec != "auto" and not _avif.encoder_codec_available(codec):
+        msg = "Invalid saving codec"
+        raise ValueError(msg)
+    range_ = info.get("range", "full")
+    tile_rows_log2 = info.get("tile_rows", 0)
+    tile_cols_log2 = info.get("tile_cols", 0)
+    alpha_premultiplied = bool(info.get("alpha_premultiplied", False))
+    autotiling = bool(info.get("autotiling", tile_rows_log2 == tile_cols_log2 == 0))
+
+    icc_profile = info.get("icc_profile", im.info.get("icc_profile"))
+    exif_orientation = 1
+    if exif := info.get("exif"):
+        if isinstance(exif, Image.Exif):
+            exif_data = exif
+        else:
+            exif_data = Image.Exif()
+            exif_data.load(exif)
+        if ExifTags.Base.Orientation in exif_data:
+            exif_orientation = exif_data.pop(ExifTags.Base.Orientation)
+            exif = exif_data.tobytes() if exif_data else b""
+        elif isinstance(exif, Image.Exif):
+            exif = exif_data.tobytes()
+
+    xmp = info.get("xmp")
+
+    if isinstance(xmp, str):
+        xmp = xmp.encode("utf-8")
+
+    advanced = info.get("advanced")
+    if advanced is not None:
+        if isinstance(advanced, dict):
+            advanced = advanced.items()
+        try:
+            advanced = tuple(advanced)
+        except TypeError:
+            invalid = True
+        else:
+            invalid = any(not isinstance(v, tuple) or len(v) != 2 for v in advanced)
+        if invalid:
+            msg = (
+                "advanced codec options must be a dict of key-value string "
+                "pairs or a series of key-value two-tuples"
+            )
+            raise ValueError(msg)
+
+    # Setup the AVIF encoder
+    enc = _avif.AvifEncoder(
+        im.size,
+        subsampling,
+        quality,
+        speed,
+        max_threads,
+        codec,
+        range_,
+        tile_rows_log2,
+        tile_cols_log2,
+        alpha_premultiplied,
+        autotiling,
+        icc_profile or b"",
+        exif or b"",
+        exif_orientation,
+        xmp or b"",
+        advanced,
+    )
+
+    # Add each frame
+    frame_idx = 0
+    frame_duration = 0
+    cur_idx = im.tell()
+    is_single_frame = total == 1
+    try:
+        for ims in [im] + append_images:
+            # Get number of frames in this image
+            nfr = getattr(ims, "n_frames", 1)
+
+            for idx in range(nfr):
+                ims.seek(idx)
+
+                # Make sure image mode is supported
+                frame = ims
+                rawmode = ims.mode
+                if ims.mode not in {"RGB", "RGBA"}:
+                    rawmode = "RGBA" if ims.has_transparency_data else "RGB"
+                    frame = ims.convert(rawmode)
+
+                # Update frame duration
+                if isinstance(duration, (list, tuple)):
+                    frame_duration = duration[frame_idx]
+                else:
+                    frame_duration = duration
+
+                # Append the frame to the animation encoder
+                enc.add(
+                    frame.tobytes("raw", rawmode),
+                    frame_duration,
+                    frame.size,
+                    rawmode,
+                    is_single_frame,
+                )
+
+                # Update frame index
+                frame_idx += 1
+
+                if not save_all:
+                    break
+
+    finally:
+        im.seek(cur_idx)
+
+    # Get the final output from the encoder
+    data = enc.finish()
+    if data is None:
+        msg = "cannot write file as AVIF (encoder returned None)"
+        raise OSError(msg)
+
+    fp.write(data)
+
+
+Image.register_open(AvifImageFile.format, AvifImageFile, _accept)
+if SUPPORTED:
+    Image.register_save(AvifImageFile.format, _save)
+    Image.register_save_all(AvifImageFile.format, _save_all)
+    Image.register_extensions(AvifImageFile.format, [".avif", ".avifs"])
+    Image.register_mime(AvifImageFile.format, "image/avif")