timewise 1.0.0a9__py3-none-any.whl → 1.0.0a10__py3-none-any.whl

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

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
         )

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/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.0a9"
+__version__ = "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/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/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/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.dist-info → timewise-1.0.0a10.dist-info}/METADATA

@@ -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.dist-info → timewise-1.0.0a10.dist-info}/RECORD

@@ -1,25 +1,25 @@
-ampel/timewise/alert/TimewiseAlertSupplier.py,sha256=zGpEaObAWWHxZ10lgDCG-uCxmGUx_tJwjfzsQqBmZYY,4200
+ampel/timewise/alert/TimewiseAlertSupplier.py,sha256=M6F0oWhPvqDpeW1S4jbfKcSXutg0wnatSFieR_Ulk5w,4216
 ampel/timewise/alert/load/TimewiseFileLoader.py,sha256=bmuKys-D7mN3FdVRoIAoOUzH_z5fTw7ph3K-rFJvdIA,4792
 ampel/timewise/ingest/TiCompilerOptions.py,sha256=j2eUxSkJEKxAjJCd9plxRRCg6Mv8dNHw72UvKyAxUsA,809
 ampel/timewise/ingest/TiDataPointShaper.py,sha256=KbAg-J0DkMaJA9K67xMY5Pe0SIP0LNKsBNAMnTYV9zA,3180
 ampel/timewise/ingest/TiMongoMuxer.py,sha256=Y0rt31FEpOd5DxI1IACI6lgNq8ruwCecU4e2nZsQuEA,11381
 ampel/timewise/ingest/tags.py,sha256=ggn0Y6QUnjIwMzOlgKmPX1JPhmnvc21nUrORFhaR0uI,564
-ampel/timewise/t1/T1HDBSCAN.py,sha256=zVhcqQVAjlHgDBd9CJA6rGH3RCrCV84rsIIOWVxODKI,9528
-ampel/timewise/t1/TimewiseFilter.py,sha256=uDjNGsqPOISoFjSH8tX87I3UTW9qGX8rEmkyze8u2ug,1566
+ampel/timewise/t1/T1HDBSCAN.py,sha256=5joN-JNtoI_9dk3Q0zl0EGL6jKNCjbz_6tBnxH8Ix0s,9584
+ampel/timewise/t1/TimewiseFilter.py,sha256=rkqI7c6x6vpRPpdVwEGvZLdvcJf8X02vsR2DjOcqki8,1571
 ampel/timewise/t2/T2StackVisits.py,sha256=JBxFZLT-a-8jjenRw45ZVA_FvtcyOBmvMVcpYHyw_Yk,2574
 ampel/timewise/util/AuxDiagnosticPlotter.py,sha256=evvuH5vuEOFkfbkoSQw7ztiEqHos19PP91VQ_SCg_AU,1692
 ampel/timewise/util/pdutil.py,sha256=CJqeYqL2I6A5WnF5S342bwM4omJY-1XwT1XWY2uk3bc,1524
-timewise/__init__.py,sha256=UBV5ucjbNEZwWwlTUO9yll_qfeL4UdJ7f9_tRHCgLds,24
+timewise/__init__.py,sha256=8zyDLNzfVXEOy1p7e1MfCjp4ljUWsoJM9LaLeealOa0,25
 timewise/backend/__init__.py,sha256=w79nWfCw8n9g98CkHWJELmb4j9xblWC4DGZOV3_XhH4,134
 timewise/backend/base.py,sha256=iZyq_avKCoLuDp6vRNITI6zStQnsBfSaF47tG7DF0Wg,1155
 timewise/backend/filesystem.py,sha256=wR1kcPWumiwgc72jBSzjbAG4PKPywre3pA4UYJwP134,2685
-timewise/chunking.py,sha256=eRd3xof-5uHaxo8Pmwo4kr_cdZSfFpgTiPu-xuL-SGA,2404
+timewise/chunking.py,sha256=C_wbfvraJ_ESIKWcGgH7Usd3cIvC9jUcE6FX8rp14Qs,2379
 timewise/cli.py,sha256=A1-glt0_JJvS8TOnNjR6jX5SaFUTGhH9p1HC_gyYpHE,4383
 timewise/config.py,sha256=ZTSokRZMZDqBqVFV9DxvO-47yE9E9xWF48Rcjb0QG10,1044
 timewise/io/__init__.py,sha256=S7vb0glKJnw6ztOlrD-0Wma2bQZ2RwpmXDLFJLKBMVo,35
 timewise/io/config.py,sha256=UEmZr-C3_TQKWSsdyFldb6pjn_s7QK9mkZar3Xzp-dM,2611
 timewise/io/download.py,sha256=FG28Tk4QDW7MZx7pi6xFuoQVcB70aTZMUzbjdFG2RJo,10842
-timewise/io/stable_tap.py,sha256=VWlKGj6WxlDIwstdDMRIhwNDZJwciaMnsBYx20Z1Uqw,4063
+timewise/io/stable_tap.py,sha256=DUDvUh3r2PiXZf-uxDfnCvdFtDmFsW58bCshvoafGWU,4806
 timewise/plot/__init__.py,sha256=cc00UenWC_8zAkBH-Ylhs3yCF49tAqZ2Al9MfOoXYDI,120
 timewise/plot/diagnostic.py,sha256=GRp-OUwz2yzzDu9qdViFg_e3Mxl5t1IvUJXZHuMKB2U,8276
 timewise/plot/lightcurve.py,sha256=K0UvjmvbCSsRKP3Mu9X5L5AVUwqURR76ESJCIMEgE6Q,3924
@@ -27,9 +27,9 @@ timewise/plot/panstarrs.py,sha256=X2ZULm7QT91cp4qociG0fVeI0saGLJwyKzL0141Vqis,80
 timewise/plot/sdss.py,sha256=xCNEKBWTn8SjC5-hEaTgV354laNEIGgCAxN8MwU9h5c,2554
 timewise/process/__init__.py,sha256=Yk-j1B1MnBuuaM6eFi43TxdWmFKbwFHvDsuQZt4yB_c,70
 timewise/process/config.py,sha256=d4hCvNb8JyJf2-0BTQgJaeOmHGZK_aHEDMb_xyqJgbU,1060
-timewise/process/interface.py,sha256=JOIh1wYuE1s9XdSfBRS7qUXexlr-p5UxdwaSjKlRZxE,5207
+timewise/process/interface.py,sha256=UXgNsIec3z8boGTyMvLUzQkNIzt4OnhFQgVKtmag_Rg,5352
 timewise/process/keys.py,sha256=MGnTHM4UGUSyX7BaCzoT_dg81NEAiLCxMLBRz3Kq8yc,319
-timewise/process/stacking.py,sha256=vVyrhrBRpqkptNryxNxWwEvXeQLH2GYNUtUxWggYfTk,18997
+timewise/process/stacking.py,sha256=9y3ZV2VW-5mv0UivfS3gjksgBr1MEtfn1ckR0r_PT4o,19032
 timewise/process/template.yml,sha256=U_xKmygDl3E-viTgZEI8pQIJwWduB52SdI2X9vy61Yo,1037
 timewise/query/__init__.py,sha256=qEVUbk20GcYOLguex1q8f0LauA2BFIWURpceuYSgMOU,327
 timewise/query/base.py,sha256=GjAoQZpaxVHcpCgPco1y5bpR0Jtd_sp_bYMI26WpAK0,1262
@@ -45,8 +45,8 @@ timewise/util/csv_utils.py,sha256=5i3Jd4c58-doPs1N_hyYZ8Uc2nvuk9nGwgPNZoNrlu0,29
 timewise/util/error_threading.py,sha256=uyV1Ri-wf87lpa17Xlp520B1V8DWHh3v9Mk97QrPmv0,2264
 timewise/util/path.py,sha256=-CcpYdjidg5FcZnRyQqrK_EKjc-7USYbJ8gtKatGl6k,254
 timewise/util/visits.py,sha256=4ZXwH7OXmp98tUPZplvuOtykB048kZoYXyuRTwQxT7w,998
-timewise-1.0.0a9.dist-info/METADATA,sha256=DmNUYj-hQOjxCmPRTOFPtanxTz_vy6ke4YCsvBOSImk,10367
-timewise-1.0.0a9.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-timewise-1.0.0a9.dist-info/entry_points.txt,sha256=mYh1HsUFbV7KT8kxiGqVtR3Pk0oEk6Bd-2c5FsYVhG4,45
-timewise-1.0.0a9.dist-info/licenses/LICENSE,sha256=sVoNJWiTlH-NarJx0wdsob468Pg3JE6vIIgll4lCa3E,1070
-timewise-1.0.0a9.dist-info/RECORD,,
+timewise-1.0.0a10.dist-info/METADATA,sha256=LZ_6JpaUoLJBGMcuPKqyhYcITucndg7RRqDvCFPvVPU,10831
+timewise-1.0.0a10.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+timewise-1.0.0a10.dist-info/entry_points.txt,sha256=mYh1HsUFbV7KT8kxiGqVtR3Pk0oEk6Bd-2c5FsYVhG4,45
+timewise-1.0.0a10.dist-info/licenses/LICENSE,sha256=sVoNJWiTlH-NarJx0wdsob468Pg3JE6vIIgll4lCa3E,1070
+timewise-1.0.0a10.dist-info/RECORD,,

{timewise-1.0.0a9.dist-info → timewise-1.0.0a10.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.1
 Root-Is-Purelib: true
 Tag: py3-none-any