timewise 1.0.0a9__tar.gz → 1.0.0a10__tar.gz

{timewise-1.0.0a9 → timewise-1.0.0a10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: timewise
-Version: 1.0.0a9
+Version: 1.0.0a10
 Summary: Download WISE infrared data for many objects and process them with AMPEL
 License: MIT
 License-File: LICENSE
@@ -15,22 +15,22 @@ Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: ampel
 Provides-Extra: dev
 Provides-Extra: docs
-Requires-Dist: ampel-alerts (==0.10.3a6) ; extra == "ampel"
-Requires-Dist: ampel-core (==0.10.6a17) ; extra == "ampel"
+Requires-Dist: ampel-alerts (==0.10.4a0) ; extra == "ampel"
+Requires-Dist: ampel-core (==0.10.6a21) ; extra == "ampel"
 Requires-Dist: ampel-interface (==0.10.5a8) ; extra == "ampel"
 Requires-Dist: ampel-photometry (==0.10.2a1) ; extra == "ampel"
 Requires-Dist: ampel-plot (>=0.9.1,<0.10.0) ; extra == "ampel"
 Requires-Dist: astropy (>=5.1,<8.0.0)
 Requires-Dist: autodoc_pydantic[erdantic] (>=2.2.0,<3.0.0) ; extra == "docs"
 Requires-Dist: backoff (>=2.1.2,<3.0.0)
-Requires-Dist: coveralls (>=3.3.1,<4.0.0) ; extra == "dev"
+Requires-Dist: coveralls (>=4.0.0,<5.0.0) ; extra == "dev"
 Requires-Dist: jupyter[jupyter] (>=1.0.0,<2.0.0)
 Requires-Dist: jupyterlab[jupyter] (>=4.0.6,<5.0.0)
 Requires-Dist: matplotlib (>=3.5.3,<4.0.0)
 Requires-Dist: mongomock (>=4.3.0,<5.0.0) ; extra == "dev"
 Requires-Dist: mypy (>=1.18.2,<2.0.0) ; extra == "dev"
 Requires-Dist: myst-parser (>=1,<3) ; extra == "docs"
-Requires-Dist: numpy (>=1.23.2,<2.0.0)
+Requires-Dist: numpy (>=1.23.2,<3.0.0)
 Requires-Dist: pandas (>=1.4.3,<3.0.0)
 Requires-Dist: pandas-stubs (>=2.3.2.250926,<3.0.0.0) ; extra == "dev"
 Requires-Dist: pydantic (>=2.0.0,<3.0.0)
@@ -38,12 +38,12 @@ Requires-Dist: pytest (>=7.2.2,<8.0.0) ; extra == "dev"
 Requires-Dist: pyvo (>=1.7.0,<2.0.0)
 Requires-Dist: requests (>=2.28.1,<3.0.0)
 Requires-Dist: ruff (>=0.13.0,<0.14.0) ; extra == "dev"
-Requires-Dist: scikit-image (>=0.19.3,<0.22.0)
+Requires-Dist: scikit-image (>=0.26.0,<0.27.0)
 Requires-Dist: scikit-learn (>=1.3.0,<2.0.0)
 Requires-Dist: scipy-stubs (>=1.16.2.0,<2.0.0.0) ; extra == "dev"
 Requires-Dist: sphinx-rtd-theme (>=1.3.0,<2.0.0) ; extra == "docs"
 Requires-Dist: tqdm (>=4.64.0,<5.0.0)
-Requires-Dist: typer (>=0.19.2,<0.20.0)
+Requires-Dist: typer (>=0.19.2,<0.30.0)
 Requires-Dist: types-pyyaml (>=6.0.12.20250915,<7.0.0.0) ; extra == "dev"
 Requires-Dist: types-requests (>=2.32.4.20250913,<3.0.0.0) ; extra == "dev"
 Requires-Dist: urllib3 (>=2.5.0,<3.0.0)
@@ -61,29 +61,31 @@ Description-Content-Type: text/markdown
 ![](timewise.png)
 # Infrared light curves from WISE data
 
-This package downloads WISE data for positions on the sky and stacks single-exposure photometry per visit
+This package downloads WISE data for positions on the sky and stacks single-exposure photometry per visit. It is designed to do so for efficiently for large samples of millions of objects.
 
 ## Prerequisites
 Python version 3.11, 3.12 or 3.13.
 
 If you want to not only download individual exposure photometry but also stack detections per visit (see below),
-you must have access to a running [MongoDB](https://www.mongodb.com/)*. 
+you must have access to a running [MongoDB](https://www.mongodb.com/)* **. 
 
 <sub>* On MacOS have alook at the custom `brew` tap 
 [here](https://github.com/mongodb/homebrew-brew)
 to get the MongoDB community edition. </sub>
 
+<sub>** On some systems this is not straight forward to set up. `timewise` requires it nevertheless as an integral part of the AMPEL system which is used to efficiently schedule and store the stacking of lightcurves. If you do not foresee a big overhead in calculating lightcurves for a sample of O(1000) objects, a more lightweight package might be more applicable. </sub>
+
 ## Installation
 
 ### If you use timewise only for downloading
 The package can be installed via `pip` (but make sure to install the v1 pre-release):
 ```bash
-pip install --pre timewise==1.0.0a9
+pip install --pre timewise==1.0.0a10
 ```
 ### If you use timewise also for stacking individual exposures
 You must install with the `ampel` extra:
 ```bash
-pip install --pre 'timewise[ampel]==1.0.0a9'
+pip install --pre 'timewise[ampel]==1.0.0a10'
 ```
 To tell AMPEL which modules, aka units, to use, build the corresponding configuration file:
 ```bash

{timewise-1.0.0a9 → timewise-1.0.0a10}/README.md

@@ -7,29 +7,31 @@
 ![](timewise.png)
 # Infrared light curves from WISE data
 
-This package downloads WISE data for positions on the sky and stacks single-exposure photometry per visit
+This package downloads WISE data for positions on the sky and stacks single-exposure photometry per visit. It is designed to do so for efficiently for large samples of millions of objects.
 
 ## Prerequisites
 Python version 3.11, 3.12 or 3.13.
 
 If you want to not only download individual exposure photometry but also stack detections per visit (see below),
-you must have access to a running [MongoDB](https://www.mongodb.com/)*. 
+you must have access to a running [MongoDB](https://www.mongodb.com/)* **. 
 
 <sub>* On MacOS have alook at the custom `brew` tap 
 [here](https://github.com/mongodb/homebrew-brew)
 to get the MongoDB community edition. </sub>
 
+<sub>** On some systems this is not straight forward to set up. `timewise` requires it nevertheless as an integral part of the AMPEL system which is used to efficiently schedule and store the stacking of lightcurves. If you do not foresee a big overhead in calculating lightcurves for a sample of O(1000) objects, a more lightweight package might be more applicable. </sub>
+
 ## Installation
 
 ### If you use timewise only for downloading
 The package can be installed via `pip` (but make sure to install the v1 pre-release):
 ```bash
-pip install --pre timewise==1.0.0a9
+pip install --pre timewise==1.0.0a10
 ```
 ### If you use timewise also for stacking individual exposures
 You must install with the `ampel` extra:
 ```bash
-pip install --pre 'timewise[ampel]==1.0.0a9'
+pip install --pre 'timewise[ampel]==1.0.0a10'
 ```
 To tell AMPEL which modules, aka units, to use, build the corresponding configuration file:
 ```bash

{timewise-1.0.0a9 → timewise-1.0.0a10}/ampel/timewise/alert/TimewiseAlertSupplier.py

@@ -9,7 +9,7 @@
 
 import sys
 from hashlib import blake2b
-from typing import Literal, List
+from typing import Literal, List, Dict, Any
 
 import pandas as pd
 
@@ -88,7 +88,7 @@ class TimewiseAlertSupplier(BaseAlertSupplier, AmpelABC):
         for i, row in table.iterrows():
             # convert table row to dict, convert data types from numpy to native python
             # Respect masked fields and convert to None
-            pp = {k: None if pd.isna(v) else v for k, v in row.to_dict().items()}
+            pp = {str(k): None if pd.isna(v) else v for k, v in row.to_dict().items()}
             pp_hash = blake2b(encode(pp), digest_size=7).digest()
             if self.counter:
                 pp["candid"] = self.counter

{timewise-1.0.0a9 → timewise-1.0.0a10}/ampel/timewise/t1/T1HDBSCAN.py

@@ -37,6 +37,7 @@ else:
 class T1HDBSCAN(AbsT1CombineUnit):
     input_mongo_db_name: str
     original_id_key: str
+    mongo: str = "mongodb://localhost:27017/"
     whitelist_region_arcsec: float = 1
     cluster_distance_arcsec: float = 0.5
 
@@ -57,7 +58,7 @@ class T1HDBSCAN(AbsT1CombineUnit):
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
-        self._col = MongoClient()[self.input_mongo_db_name]["input"]
+        self._col = MongoClient(self.mongo)[self.input_mongo_db_name]["input"]
         self._plotter = AuxUnitRegister.new_unit(
             model=self.plotter, sub_type=AuxDiagnosticPlotter
         )

{timewise-1.0.0a9 → timewise-1.0.0a10}/ampel/timewise/t1/TimewiseFilter.py

@@ -17,7 +17,7 @@ from timewise.process import keys
 
 class TimewiseFilter(AbsAlertFilter):
     det_per_visit: int = 8
-    n_visits = 10
+    n_visits: int = 10
 
     def process(self, alert: AmpelAlertProtocol) -> None | bool | int:
         columns = [

{timewise-1.0.0a9 → timewise-1.0.0a10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "timewise"
-version = "1.0.0a9"
+version = "1.0.0a10"
 description = "Download WISE infrared data for many objects and process them with AMPEL"
 authors = [
     { name = "Jannis Necker", email = "jannis.necker@gmail.com" },
@@ -16,18 +16,18 @@ dependencies = [
     "tqdm>=4.64.0,<5.0.0",
     "requests>=2.28.1,<3.0.0",
     "pandas>=1.4.3,<3.0.0",
-    "numpy>=1.23.2,<2.0.0",
+    "numpy>=1.23.2,<3.0.0",
     "pyvo>=1.7.0,<2.0.0",
     "astropy>=5.1,<8.0.0",
     "matplotlib>=3.5.3,<4.0.0",
-    "scikit-image>=0.19.3,<0.22.0",
+    "scikit-image>=0.26.0,<0.27.0",
     "backoff>=2.1.2,<3.0.0",
     "virtualenv>=20.16.3,<21.0.0",
     "pydantic>=2.0.0,<3.0.0",
     "scikit-learn>=1.3.0,<2.0.0",
     "jupyterlab[jupyter]>=4.0.6,<5.0.0",
     "jupyter[jupyter]>=1.0.0,<2.0.0",
-    "typer (>=0.19.2,<0.20.0)",
+    "typer (>=0.19.2,<0.30.0)",
     "urllib3 (>=2.5.0,<3.0.0)",
 ]
 
@@ -46,7 +46,7 @@ Homepage = "https://github.com/JannisNe/timewise"
 
 [project.optional-dependencies]
 dev = [
-    "coveralls>=3.3.1,<4.0.0",
+    "coveralls>=4.0.0,<5.0.0",
     "pytest>=7.2.2,<8.0.0",
     "ruff>=0.13.0,<0.14.0",
     "mypy (>=1.18.2,<2.0.0)",
@@ -64,8 +64,8 @@ docs = [
 ampel= [
     "ampel-photometry (==0.10.2a1)",
     "ampel-plot (>=0.9.1,<0.10.0)",
-    "ampel-core (==0.10.6a17)",
-    "ampel-alerts (==0.10.3a6)",
+    "ampel-core (==0.10.6a21)",
+    "ampel-alerts (==0.10.4a0)",
     "ampel-interface (==0.10.5a8)"
 ]
 

timewise-1.0.0a10/timewise/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0a10"

{timewise-1.0.0a9 → timewise-1.0.0a10}/timewise/chunking.py

@@ -11,9 +11,7 @@ logger = logging.getLogger(__name__)
 
 
 class Chunk:
-    def __init__(
-        self, chunk_id: int, input_csv, row_indices: npt.NDArray[np.int_]
-    ):
+    def __init__(self, chunk_id: int, input_csv, row_indices: npt.NDArray[np.int_]):
         self.chunk_id = chunk_id
         self.row_numbers = row_indices
         self.input_csv = input_csv
@@ -71,4 +69,4 @@ class Chunker:
         start = chunk_id * self.chunk_size
         stop = min(start + self.chunk_size, self._n_rows)
         logger.debug(f"chunk {chunk_id}: from {start} to {stop}")
-        return Chunk(chunk_id, self.input_csv, np.arange(start=start, stop=stop))
+        return Chunk(chunk_id, self.input_csv, np.arange(start, stop))

{timewise-1.0.0a9 → timewise-1.0.0a10}/timewise/io/stable_tap.py

@@ -95,10 +95,32 @@ class StableAsyncTAPJob(vo.dal.AsyncTAPJob):
     @backoff.on_exception(
         backoff.expo,
         vo.dal.DALServiceError,
-        max_tries=50,
+        max_tries=5,
     )
-    def _update(self, *args, **kwargs):
-        return super(StableAsyncTAPJob, self)._update(*args, **kwargs)
+    def _update(self, wait_for_statechange=False, timeout=60.0):
+        n_tries = 0
+        max_tries = 10
+        while n_tries < max_tries:
+            try:
+                res = super(StableAsyncTAPJob, self)._update(
+                    wait_for_statechange=wait_for_statechange,
+                    timeout=timeout * (1 + n_tries),
+                )
+            except vo.dal.DALServiceError as e:
+                if "Read timed out" in str(e):
+                    logger.debug(
+                        f"{self.url} timed out after {timeout * (1 + n_tries):.0f}s"
+                    )
+                    n_tries += 1
+                    continue
+                else:
+                    raise e
+
+            return res
+
+        raise vo.dal.DALServiceError(
+            f"No success after {max_tries} tries for {self.url}!"
+        )
 
 
 class StableTAPService(vo.dal.TAPService):
@@ -136,6 +158,8 @@ class StableTAPService(vo.dal.TAPService):
         max_tries=5,
     )
     def run_sync(
-            self, query, *, language="ADQL", maxrec=None, uploads=None,
-            **keywords):
-        return super().run_sync(query, language=language, maxrec=maxrec, uploads=uploads, **keywords)
+        self, query, *, language="ADQL", maxrec=None, uploads=None, **keywords
+    ):
+        return super().run_sync(
+            query, language=language, maxrec=maxrec, uploads=uploads, **keywords
+        )

{timewise-1.0.0a9 → timewise-1.0.0a10}/timewise/process/interface.py

@@ -10,6 +10,8 @@ from pymongo import MongoClient, ASCENDING
 from pymongo.collection import Collection
 from pymongo.database import Database
 
+from ..util.path import expand
+
 if find_spec("ampel.core"):
     AMPEL_EXISTS = True
     from ampel.cli.JobCommand import JobCommand
@@ -40,6 +42,10 @@ class AmpelInterface:
         self.template_path = Path(template_path)
         self.uri = uri
 
+    @property
+    def expanded_input_csv(self) -> Path:
+        return expand(self.input_csv)
+
     def import_input(self):
         # if collection already exists, assume import was already done
         if "input" in self.client[self.input_mongo_db_name].list_collection_names():
@@ -48,12 +54,12 @@ class AmpelInterface:
             )
             return
 
-        logger.debug(f"importing {self.input_csv} into {self.input_mongo_db_name}")
+        logger.debug(f"importing {self.expanded_input_csv} into {self.input_mongo_db_name}")
         col = self.client[self.input_mongo_db_name]["input"]
 
         # create an index from stock id
         col.create_index([(self.orig_id_key, ASCENDING)], unique=True)
-        col.insert_many(pd.read_csv(self.input_csv).to_dict(orient="records"))
+        col.insert_many(pd.read_csv(self.expanded_input_csv).to_dict(orient="records"))
 
     def make_ampel_job_file(self, cfg_path: Path) -> Path:
         logger.debug(f"loading ampel job template from {self.template_path}")

{timewise-1.0.0a9 → timewise-1.0.0a10}/timewise/process/stacking.py

@@ -146,7 +146,7 @@ def calculate_epochs(
     bias_correction_function = CORRECTION_FUNCTIONS[correction_name]
 
     one_points_mask = None
-    visits_at_least_two_point = []
+    visits_at_least_two_point: npt.NDArray[np.generic] = np.array([])
 
     while n_remaining_outlier > 0:
         # make a mask of values to use

timewise-1.0.0a9/timewise/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.0.0a9"