atomscale 0.8.0__tar.gz → 0.8.2__tar.gz

{atomscale-0.8.0 → atomscale-0.8.2}/.github/workflows/release.yml

@@ -139,17 +139,21 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements/requirements-ubuntu-latest_py3.11.txt
-          pip install -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
-          pip install sphinx
-          pip install -e .
+          uv pip install --system -r requirements/requirements-ubuntu-latest_py3.11.txt
+          uv pip install --system -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
+          uv pip install --system -e .
 
       - name: Build docs
         run: sphinx-build ./docs ./docs/_build

{atomscale-0.8.0 → atomscale-0.8.2}/.github/workflows/testing.yml

@@ -17,30 +17,24 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements/requirements-ubuntu-latest_py3.11.txt
-          pip install -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
-
       - name: Install dependencies
         run: |
-          pip install pre-commit
+          uv pip install --system -r requirements/requirements-ubuntu-latest_py3.11.txt
+          uv pip install --system -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
+          uv pip install --system pre-commit ty
 
       - name: Run pre-commit
-        run: |
-          pre-commit run --all-files --show-diff-on-failure
-
-      - name: Run mypy
-        run: |
-          mypy --version
-          rm -rf .mypy_cache
-          mypy src/atomicds
+        run: pre-commit run --all-files --show-diff-on-failure
 
   test:
     needs: lint
@@ -55,16 +49,20 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Python dependencies
+      - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}.txt
-          pip install -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
+          uv pip install --system -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}.txt
+          uv pip install --system -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
 
       - name: Set SSL_CERT_FILE (Linux/MacOS)
         if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
@@ -74,13 +72,14 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: echo "SSL_CERT_FILE=$(python -m certifi)" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
 
+      - name: Install package
+        run: uv pip install --system -e .
+
       - name: Test with pytest
         env:
           AS_API_KEY: ${{ secrets.AS_API_KEY }}
           AS_API_ENDPOINT: "https://api.atomscale.ai"
-        run: |
-          pip install -e .
-          pytest -x
+        run: pytest -x
 
   auto-gen-release:
     needs: test

{atomscale-0.8.0 → atomscale-0.8.2}/.pre-commit-config.yaml

@@ -5,19 +5,8 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
 
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-
-  - repo: https://github.com/asottile/blacken-docs
-    rev: "1.16.0"
-    hooks:
-      - id: blacken-docs
-        additional_dependencies: [black>=23.7.0]
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -28,15 +17,27 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.9.4
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
+        exclude: '\.ipynb$'
+      - id: ruff-format
+        exclude: '\.ipynb$'
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
         exclude_types: [json, bib, svg]
         args: [--ignore-words-list, "mater,fwe,te"]
+
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty
+        entry: ty check src/atomicds
+        language: system
+        types: [python]
+        pass_filenames: false

{atomscale-0.8.0/src/atomscale.egg-info → atomscale-0.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: atomscale
-Version: 0.8.0
+Version: 0.8.2
 Summary: Python SDK for Atomscale.
 Author-email: Atomscale <info@atomscale.ai>
 License: GPL-3.0-only
@@ -36,10 +36,11 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-order; extra == "dev"
 Requires-Dist: pytest-dependency; extra == "dev"
 Requires-Dist: pytest-asyncio; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: mypy; extra == "dev"
+Requires-Dist: ruff>=0.9.0; extra == "dev"
+Requires-Dist: ty; extra == "dev"
 Requires-Dist: types-requests; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
+Requires-Dist: pre-commit>=4.0.0; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx>=6.2; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints>=1.24; extra == "docs"

{atomscale-0.8.0 → atomscale-0.8.2}/pyproject.toml

@@ -49,10 +49,11 @@ dev = [
   "pytest-order",
   "pytest-dependency",
   "pytest-asyncio",
-  "ruff",
-  "mypy",
+  "ruff>=0.9.0",
+  "ty",
   "types-requests",
   "pandas-stubs",
+  "pre-commit>=4.0.0",
 ]
 docs = ["sphinx>=6.2", "sphinx-autodoc-typehints>=1.24", "alabaster>=0.7"]
 
@@ -73,10 +74,6 @@ path = "src/atomscale/streaming/Cargo.toml"
 binding = "PyO3"
 
 
-[tool.pyright]
-include = ["atomscale", "atomicds"]
-exclude = ["**/__pycache__"]
-
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = ["-p no:warnings", "--import-mode=importlib"]
@@ -84,18 +81,6 @@ xfail_strict = true
 log_cli_level = "warn"
 testpaths = ["tests"]
 
-[tool.black]
-exclude = '''
-/(
-    \.git
-  | \.tox
-)/
-'''
-
-[tool.isort]
-profile = 'black'
-skip_gitignore = true
-
 [tool.coverage.run]
 source = ["src"]
 
@@ -137,11 +122,9 @@ lint.select = [
 lint.extend-ignore = [
   "PLR",   # Design related pylint codes
   "E501",  # Line too long
-  "PT004", # Use underscore for non-returning fixture (use usefixture instead)
   "B028",  # No explicit stacklevel
   "EM101", # Exception must not use a string literal
   "EM102", # Exception must not use an f-string literal
-  "PD901", # Avoid using the generic variable name `df` for DataFrames
 ]
 lint.typing-modules = ["mypackage._compat.typing"]
 src = ["src"]
@@ -151,20 +134,19 @@ lint.unfixable = [
 ]
 exclude = []
 lint.flake8-unused-arguments.ignore-variadic-names = true
-extend-exclude = ["tests"]
+extend-exclude = ["tests", "examples", "*.ipynb"]
 lint.pydocstyle.convention = "google"
 lint.isort.known-first-party = ["atomscale"]
 
 [tool.docformatter]
 pre-summary-newline = true
-black = true
-
-[tool.mypy]
-ignore_missing_imports = true
-namespace_packages = true
-explicit_package_bases = true
-no_implicit_optional = false
-disable_error_code = "annotation-unchecked"
+
+[tool.ty.environment]
+root = ["./src"]
+
+[tool.ty.src]
+include = ["src/atomicds"]
+exclude = ["tests", "examples", "docs"]
 
 [tool.codespell]
 ignore-words-list = "fpr"

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/core/client.py

@@ -245,9 +245,9 @@ class BaseClient:
         atomscale_info = "atomscale/" + __version__
         python_info = f"Python/{sys.version.split()[0]}"
         platform_info = f"{platform.system()}/{platform.release()}"
-        session.headers[
-            "user-agent"
-        ] = f"{atomscale_info} ({python_info} {platform_info})"
+        session.headers["user-agent"] = (
+            f"{atomscale_info} ({python_info} {platform_info})"
+        )
 
         # TODO: Add retry setting to configuration somewhere
         max_retry_num = 3

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/results/__init__.py

@@ -5,6 +5,7 @@ from .photoluminescence import PhotoluminescenceResult
 from .raman import RamanResult
 from .rheed_image import RHEEDImageCollection, RHEEDImageResult, _get_rheed_image_result
 from .rheed_video import RHEEDVideoResult
+from .similarity_trajectory import SimilarityTrajectoryResult
 from .unknown import UnknownResult
 from .xps import XPSResult
 
@@ -18,7 +19,8 @@ __all__ = [
     "RHEEDImageResult",
     "RHEEDVideoResult",
     "RamanResult",
-    "XPSResult",
+    "SimilarityTrajectoryResult",
     "UnknownResult",
+    "XPSResult",
     "_get_rheed_image_result",
 ]

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/results/rheed_image.py

@@ -371,9 +371,7 @@ class RHEEDImageResult(MSONable):
                 x,
                 new_df["mask_height"].iloc[0],  # type: ignore  # noqa: PGH003
                 new_df["mask_width"].iloc[0],  # type: ignore  # noqa: PGH003
-            )[
-                "counts"
-            ]
+            )["counts"]
 
             new_df = new_df.groupby("node_id").agg(agg_dict).reset_index(drop=True)
 

atomscale-0.8.2/src/atomscale/results/similarity_trajectory.py

@@ -0,0 +1,34 @@
+from __future__ import annotations
+
+from collections.abc import Sequence
+from uuid import UUID
+
+from monty.json import MSONable
+from pandas import DataFrame
+
+
+class SimilarityTrajectoryResult(MSONable):
+    def __init__(
+        self,
+        source_id: UUID | str,
+        workflow: str,
+        window_span: float,
+        timeseries_data: DataFrame,
+        source_data_ids: Sequence[UUID | str] | None = None,
+    ):
+        """Similarity trajectory result
+
+        Args:
+            source_id (UUID | str): Source ID for the similarity trajectory query.
+            workflow (str): Workflow name used for the similarity analysis.
+            window_span (float): Window span parameter used for the trajectory.
+            timeseries_data (DataFrame): Pandas DataFrame with similarity trajectory data.
+            source_data_ids (Sequence[UUID | str] | None): Sequence of source data IDs included in the trajectory.
+        """
+        self.source_id = source_id
+        self.workflow = workflow
+        self.window_span = window_span
+        self.timeseries_data = timeseries_data
+        self.source_data_ids: list[UUID | str] = (
+            list(source_data_ids) if source_data_ids else []
+        )

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/timeseries/__init__.py

@@ -4,11 +4,13 @@ from .optical import OpticalProvider
 from .provider import TimeseriesProvider
 from .registry import get_provider
 from .rheed import RHEEDProvider
+from .similarity import SimilarityTrajectoryProvider
 
 __all__ = [
     "MetrologyProvider",
     "OpticalProvider",
     "RHEEDProvider",
+    "SimilarityTrajectoryProvider",
     "TimeseriesProvider",
     "align_timeseries",
     "get_provider",

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/timeseries/align.py

@@ -71,26 +71,26 @@ def _extract_timeseries(result):
     """Return (data_id, domain, df_with_timeindex) or None for non-timeseries."""
     if isinstance(result, RHEEDVideoResult):
         domain = "rheed"
-        df = result.timeseries_data
+        timeseries = result.timeseries_data
     elif isinstance(result, OpticalResult):
         domain = "optical"
-        df = result.timeseries_data
+        timeseries = result.timeseries_data
     elif isinstance(result, MetrologyResult):
         domain = "metrology"
-        df = result.timeseries_data
+        timeseries = result.timeseries_data
     else:
         return None
 
-    if df is None or df.empty:
+    if timeseries is None or timeseries.empty:
         return None
 
     # Build time index: prefer absolute epochs; fall back to upload_datetime + relative offsets.
     upload_dt = getattr(result, "upload_datetime", None)
 
-    time_index = _infer_absolute_time(df)
+    time_index = _infer_absolute_time(timeseries)
     if time_index is None and upload_dt is not None:
         base = pd.to_datetime(upload_dt, utc=True, errors="coerce")
-        rel = _infer_relative_time(df)
+        rel = _infer_relative_time(timeseries)
         if base is not pd.NaT and rel is not None:
             time_index = base + rel
 
@@ -101,7 +101,7 @@ def _extract_timeseries(result):
     if not valid_mask.any():
         return None
 
-    indexed = df.loc[valid_mask].copy(deep=False)
+    indexed = timeseries.loc[valid_mask].copy(deep=False)
     indexed.index = pd.Index(time_index[valid_mask], name="time")
     indexed = indexed.sort_index()
 
@@ -173,11 +173,11 @@ def align_timeseries(
         if not extracted:
             continue
 
-        data_id, domain, df = extracted
-        df = df.copy(deep=False)
-        df.columns = pd.MultiIndex.from_product([[data_id], [domain], df.columns])
-        frames.append(df)
-        indices.append(df.index)
+        data_id, domain, frame = extracted
+        frame = frame.copy(deep=False)
+        frame.columns = pd.MultiIndex.from_product([[data_id], [domain], frame.columns])
+        frames.append(frame)
+        indices.append(frame.index)
 
     if not frames:
         return pd.DataFrame()
@@ -211,11 +211,11 @@ def align_timeseries(
 
     # Merge compatible metrics across items: if multiple columns share (domain, metric)
     # and never conflict where they overlap, collapse into (shared, domain, metric).
-    def _merge_compatible_metrics(df: pd.DataFrame) -> pd.DataFrame:
-        if not isinstance(df.columns, pd.MultiIndex):
-            return df
-        domains = df.columns.get_level_values(1)
-        metrics = df.columns.get_level_values(2)
+    def _merge_compatible_metrics(data: pd.DataFrame) -> pd.DataFrame:
+        if not isinstance(data.columns, pd.MultiIndex):
+            return data
+        domains = data.columns.get_level_values(1)
+        metrics = data.columns.get_level_values(2)
         new_cols: dict = {}
         drop_cols: list = []
 
@@ -223,16 +223,16 @@ def align_timeseries(
             for metric in metrics.unique():
                 cols = [
                     c
-                    for c in df.columns
+                    for c in data.columns
                     if c[1] == domain and c[2] == metric and c[0] != "shared"
                 ]
                 if len(cols) <= 1:
                     continue
 
-                merged = df[cols[0]]
+                merged = data[cols[0]]
                 conflict = False
                 for c in cols[1:]:
-                    other = df[c]
+                    other = data[c]
                     overlap_mask = merged.notna() & other.notna()
                     if (merged[overlap_mask] != other[overlap_mask]).any():
                         conflict = True
@@ -247,10 +247,10 @@ def align_timeseries(
                 drop_cols.extend(cols)
 
         if new_cols:
-            df = df.drop(columns=drop_cols)
+            data = data.drop(columns=drop_cols)
             for col, series in new_cols.items():
-                df[col] = series
-            df = df.sort_index(axis=1)
-        return df
+                data[col] = series
+            data = data.sort_index(axis=1)
+        return data
 
     return _merge_compatible_metrics(aligned)

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/timeseries/registry.py

@@ -4,11 +4,13 @@ from .metrology import MetrologyProvider
 from .optical import OpticalProvider
 from .provider import TimeseriesProvider
 from .rheed import RHEEDProvider
+from .similarity import SimilarityTrajectoryProvider
 
 _PROVIDER_CLASSES: dict[str, type[TimeseriesProvider]] = {
     RHEEDProvider.TYPE: RHEEDProvider,
     OpticalProvider.TYPE: OpticalProvider,
     MetrologyProvider.TYPE: MetrologyProvider,
+    SimilarityTrajectoryProvider.TYPE: SimilarityTrajectoryProvider,
 }
 
 

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale/timeseries/rheed.py

@@ -41,8 +41,13 @@ class RHEEDProvider(TimeseriesProvider[RHEEDVideoResult]):
         "first_order_fwhm_1": "First Order FWHM",
         "lattice_spacing": "Lattice Spacing",
         "tar_metric": "TAR Metric",
+        "composition_metric": "Composition Metric",
     }
-    DROP_IF_ALL_NA: Sequence[str] = ["reconstruction_intensity", "tar_metric"]
+    DROP_IF_ALL_NA: Sequence[str] = [
+        "reconstruction_intensity",
+        "tar_metric",
+        "composition_metric",
+    ]
     INDEX_COLS: Sequence[str] = ["Angle", "Frame Number"]
 
     def fetch_raw(self, client: BaseClient, data_id: str, **kwargs) -> Any:

atomscale-0.8.2/src/atomscale/timeseries/similarity.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+from collections.abc import Mapping, Sequence
+from typing import Any
+from uuid import UUID
+
+from pandas import DataFrame, concat
+
+from atomscale.core import BaseClient
+from atomscale.results.similarity_trajectory import SimilarityTrajectoryResult
+from atomscale.timeseries.provider import TimeseriesProvider
+
+
+class SimilarityTrajectoryProvider(TimeseriesProvider[SimilarityTrajectoryResult]):
+    TYPE = "similarity_trajectory"
+
+    RENAME_MAP: Mapping[str, str] = {
+        "reference_id": "Reference ID",
+        "reference_item_name": "Reference Name",
+        "real_time_seconds": "Time",
+        "similarity_values": "Similarity",
+        "unix_times": "UNIX Timestamp",
+        "is_active": "Active",
+        "averaged_count": "Averaged Count",
+    }
+    INDEX_COLS: Sequence[str] = ["Reference ID", "Time"]
+
+    def fetch_raw(self, client: BaseClient, data_id: str, **kwargs: Any) -> Any:
+        """Fetch similarity trajectory data from the API.
+
+        Args:
+            client: The API client.
+            data_id: The source ID for the similarity query.
+            **kwargs: Must include 'workflow' (required). Optional parameters:
+                window_span, reference_ids, softmax_mode, reference_n_values.
+
+        Returns:
+            Raw API response payload.
+
+        Raises:
+            KeyError: If 'workflow' is not provided in kwargs.
+        """
+        workflow = kwargs.pop("workflow")
+        return client._get(
+            sub_url=f"similarity/{workflow}/{data_id}/trajectory/",
+            params=kwargs,
+        )
+
+    def to_dataframe(self, raw: Any) -> DataFrame:
+        if not raw:
+            return DataFrame(None)
+
+        trajectories = raw.get("trajectories", [])
+        if not trajectories:
+            return DataFrame(None)
+
+        frames: list[DataFrame] = []
+        for traj in trajectories:
+            ref_id = traj.get("reference_id")
+            ref_name = traj.get("reference_item_name")
+            similarity_values = traj.get("similarity_values", [])
+            real_time_seconds = traj.get("real_time_seconds", [])
+            unix_times = traj.get("unix_times", [])
+            is_active = traj.get("is_active")
+            averaged_count = traj.get("averaged_count")
+
+            if not similarity_values:
+                continue
+
+            # Build dataframe from columnar data
+            traj_df = DataFrame(
+                {
+                    "reference_id": ref_id,
+                    "reference_item_name": ref_name,
+                    "similarity_values": similarity_values,
+                    "real_time_seconds": real_time_seconds,
+                    "unix_times": unix_times,
+                    "is_active": is_active,
+                    "averaged_count": averaged_count,
+                }
+            )
+            frames.append(traj_df)
+
+        if not frames:
+            return DataFrame(None)
+
+        df_all = concat(frames, axis=0, ignore_index=True)
+        df_all = df_all.rename(columns=self.RENAME_MAP)
+
+        idx_cols = [c for c in self.INDEX_COLS if c in df_all.columns]
+        if idx_cols:
+            df_all = df_all.set_index(idx_cols)
+
+        return df_all
+
+    def build_result(
+        self,
+        client: BaseClient,  # noqa: ARG002
+        data_id: str,
+        data_type: str,  # noqa: ARG002
+        ts_df: DataFrame,
+        *,
+        workflow: str = "",
+        window_span: float = 0.0,
+        source_data_ids: Sequence[UUID | str] | None = None,
+    ) -> SimilarityTrajectoryResult:
+        return SimilarityTrajectoryResult(
+            source_id=data_id,
+            workflow=workflow,
+            window_span=window_span,
+            timeseries_data=ts_df,
+            source_data_ids=source_data_ids,
+        )

{atomscale-0.8.0 → atomscale-0.8.2/src/atomscale.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: atomscale
-Version: 0.8.0
+Version: 0.8.2
 Summary: Python SDK for Atomscale.
 Author-email: Atomscale <info@atomscale.ai>
 License: GPL-3.0-only
@@ -36,10 +36,11 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-order; extra == "dev"
 Requires-Dist: pytest-dependency; extra == "dev"
 Requires-Dist: pytest-asyncio; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: mypy; extra == "dev"
+Requires-Dist: ruff>=0.9.0; extra == "dev"
+Requires-Dist: ty; extra == "dev"
 Requires-Dist: types-requests; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
+Requires-Dist: pre-commit>=4.0.0; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx>=6.2; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints>=1.24; extra == "docs"

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale.egg-info/SOURCES.txt

@@ -73,6 +73,7 @@ src/atomscale/results/photoluminescence.py
 src/atomscale/results/raman.py
 src/atomscale/results/rheed_image.py
 src/atomscale/results/rheed_video.py
+src/atomscale/results/similarity_trajectory.py
 src/atomscale/results/unknown.py
 src/atomscale/results/xps.py
 src/atomscale/streaming/Cargo.lock
@@ -92,6 +93,7 @@ src/atomscale/timeseries/provider.py
 src/atomscale/timeseries/registry.py
 src/atomscale/timeseries/rheed.py
 src/atomscale/timeseries/sample.py
+src/atomscale/timeseries/similarity.py
 tests/__init__.py
 tests/conftest.py
 tests/test_atomicds_alias.py
@@ -104,5 +106,6 @@ tests/test_polling.py
 tests/test_raman.py
 tests/test_rheed_image.py
 tests/test_rheed_video.py
+tests/test_similarity_trajectory.py
 tests/test_xps.py
 tests/data/test_rheed.mp4

{atomscale-0.8.0 → atomscale-0.8.2}/src/atomscale.egg-info/requires.txt

@@ -16,10 +16,11 @@ pytest-cov
 pytest-order
 pytest-dependency
 pytest-asyncio
-ruff
-mypy
+ruff>=0.9.0
+ty
 types-requests
 pandas-stubs
+pre-commit>=4.0.0
 
 [docs]
 sphinx>=6.2

{atomscale-0.8.0 → atomscale-0.8.2}/tests/conftest.py

@@ -27,3 +27,5 @@ class ResultIDs:
     metrology = ""
     photoluminescence = ""
     raman = ""
+    similarity_workflow = "rheed_stationary"
+    similarity_source_id = "bb3494b1-b5fb-4f3e-ac50-e4024f8aacf5"

{atomscale-0.8.0 → atomscale-0.8.2}/tests/test_rheed_video.py

@@ -22,6 +22,7 @@ def result(client: Client):
 
 
 def test_get_dataframe(result: RHEEDVideoResult):
+    # Core columns that should always be present
     column_names = set(
         [
             "Strain",
@@ -38,9 +39,12 @@ def test_get_dataframe(result: RHEEDVideoResult):
             "Half Order Intensity R",
             "Specular FWHM",
             "First Order FWHM",
-            "Time",
             "UNIX Timestamp",
             "Relative Time",
+            # Optional columns (included if data exists)
+            "Time",
+            "TAR Metric",
+            "Composition Metric",
         ]
     )
 

atomscale-0.8.2/tests/test_similarity_trajectory.py

@@ -0,0 +1,97 @@
+import pytest
+from pandas import DataFrame
+
+from atomscale import Client
+from atomscale.results import SimilarityTrajectoryResult
+from atomscale.timeseries.similarity import SimilarityTrajectoryProvider
+
+from .conftest import ResultIDs
+
+
+@pytest.fixture
+def client():
+    return Client()
+
+
+@pytest.fixture
+def provider():
+    return SimilarityTrajectoryProvider()
+
+
+@pytest.fixture
+def raw_data(client: Client, provider: SimilarityTrajectoryProvider):
+    if not ResultIDs.similarity_workflow or not ResultIDs.similarity_source_id:
+        pytest.skip("No similarity trajectory data available")
+
+    data = provider.fetch_raw(
+        client,
+        ResultIDs.similarity_source_id,
+        workflow=ResultIDs.similarity_workflow,
+    )
+
+    if not data or not data.get("trajectories"):
+        pytest.skip("No trajectory data returned from API")
+
+    return data
+
+
+@pytest.fixture
+def result(
+    client: Client, provider: SimilarityTrajectoryProvider, raw_data: dict
+) -> SimilarityTrajectoryResult:
+    df = provider.to_dataframe(raw_data)
+    return provider.build_result(
+        client=client,
+        data_id=ResultIDs.similarity_source_id,
+        data_type="similarity_trajectory",
+        ts_df=df,
+        workflow=ResultIDs.similarity_workflow,
+    )
+
+
+def test_type_constant():
+    """Verify TYPE constant is set correctly."""
+    assert SimilarityTrajectoryProvider.TYPE == "similarity_trajectory"
+
+
+def test_fetch_raw(raw_data: dict):
+    """Verify raw data is fetched from API."""
+    assert raw_data is not None
+    assert "trajectories" in raw_data
+
+
+def test_to_dataframe(provider: SimilarityTrajectoryProvider, raw_data: dict):
+    """Verify dataframe conversion."""
+    df = provider.to_dataframe(raw_data)
+
+    assert isinstance(df, DataFrame)
+    assert not df.empty
+
+
+def test_to_dataframe_columns(provider: SimilarityTrajectoryProvider, raw_data: dict):
+    """Verify column names and index."""
+    df = provider.to_dataframe(raw_data)
+
+    # Check index names
+    assert df.index.names == ["Reference ID", "Time"]
+
+    # Check expected columns exist
+    expected_columns = {"Similarity", "Reference Name", "UNIX Timestamp", "Active", "Averaged Count"}
+    assert expected_columns == set(df.columns)
+
+
+def test_build_result(result: SimilarityTrajectoryResult):
+    """Verify result object construction."""
+    assert isinstance(result, SimilarityTrajectoryResult)
+    assert result.source_id == ResultIDs.similarity_source_id
+    assert result.workflow == ResultIDs.similarity_workflow
+    assert isinstance(result.timeseries_data, DataFrame)
+
+
+def test_result_dataframe(result: SimilarityTrajectoryResult):
+    """Verify result contains valid timeseries data."""
+    df = result.timeseries_data
+
+    assert isinstance(df, DataFrame)
+    if df.index.names != [None]:
+        assert df.index.names == ["Reference ID", "Time"]