scikit-diveMove 0.4.0__tar.gz → 1.0.0__tar.gz

scikit_divemove-1.0.0/PKG-INFO

@@ -0,0 +1,28 @@
+Metadata-Version: 2.4
+Name: scikit-diveMove
+Version: 1.0.0
+Summary: Python interface to R package diveMove
+License: AGPL-3.0-or-later
+License-File: LICENSE
+Keywords: animal behaviour,biology,behavioural ecology,diving,diving behaviour
+Author: Sebastian Luque
+Requires-Python: >=3.11
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Instrument Drivers
+Requires-Dist: bottleneck (>=1.6.0,<2.0.0)
+Requires-Dist: docutils (>=0.22.4,<0.23.0)
+Requires-Dist: matplotlib (>=3.10.8,<4.0.0)
+Requires-Dist: netcdf4 (>=1.7.4,<2.0.0)
+Requires-Dist: numpy (>=2.4.3,<3.0.0)
+Requires-Dist: pandas (>=3.0.1,<4.0.0)
+Requires-Dist: rpy2 (>=3.6.5,<4.0.0)
+Requires-Dist: scipy (>=1.17.1,<2.0.0)
+Requires-Dist: statsmodels (>=0.14.6,<0.15.0)
+Requires-Dist: xarray (>=2026.2.0,<2027.0.0)
+Project-URL: Documentation, https://spluque.github.io/scikit-diveMove
+Project-URL: Repository, https://github.com/spluque/scikit-diveMove

scikit_divemove-1.0.0/pyproject.toml

@@ -0,0 +1,85 @@
+[project]
+name = "scikit-diveMove"
+dynamic = []
+description = "Python interface to R package diveMove"
+authors = [
+    {name = "Sebastian Luque"}
+]
+license = {text = "AGPL-3.0-or-later"}
+requires-python = ">=3.11"
+dependencies = [
+    "bottleneck (>=1.6.0,<2.0.0)",
+    "docutils (>=0.22.4,<0.23.0)",
+    "matplotlib (>=3.10.8,<4.0.0)",
+    "netcdf4 (>=1.7.4,<2.0.0)",
+    "numpy (>=2.4.3,<3.0.0)",
+    "pandas (>=3.0.1,<4.0.0)",
+    "rpy2 (>=3.6.5,<4.0.0)",
+    "scipy (>=1.17.1,<2.0.0)",
+    "statsmodels (>=0.14.6,<0.15.0)",
+    "xarray (>=2026.2.0,<2027.0.0)"
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Instrument Drivers"
+]
+keywords = ["animal behaviour",
+	    "biology",
+	    "behavioural ecology",
+            "diving",
+	    "diving behaviour"
+]
+version = "1.0.0"
+
+[project.urls]
+repository = "https://github.com/spluque/scikit-diveMove"
+documentation = "https://spluque.github.io/scikit-diveMove"
+
+[dependency-groups]
+docs = [
+    "ipykernel (>=7.2.0,<8.0.0)",
+    "myst-nb (>=1.4.0,<2.0.0)",
+    "pydata-sphinx-theme (>=0.16.1,<0.17.0)"
+]
+test = [
+    "pytest (>=9.0.2,<10.0.0)",
+    "coverage (>=7.13.5,<8.0.0)"
+]
+
+[tool.poetry]
+packages = [ {include = "skdiveMove"} ]
+include = [
+    "skdiveMove/tests/data/*.db",
+    "skdiveMove/tests/data/*.txt",
+    "skdiveMove/tests/data/*.csv",
+    "skdiveMove/tests/data/*.nc",
+    "skdiveMove/config_examples/*.json"
+]
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.requires-plugins]
+poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = ["plugin"] }
+
+[tool.poetry-dynamic-versioning]
+enable = false
+
+[tool.poetry-dynamic-versioning.from-file]
+source = "skdiveMove/__init__.py"
+pattern = "^__version__\\s*=\\s*['\"](?P<version>.+?)['\"]"
+
+[build-system]
+requires = [
+    "poetry-core>=2.0.0,<3.0.0",
+    "poetry-dynamic-versioning>=1.0.0,<2.0.0"
+]
+build-backend = "poetry_dynamic_versioning.backend"

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/__init__.py

@@ -88,5 +88,5 @@ from skdiveMove.calibconfig import dump_config_template
 
 __author__ = "Sebastian Luque <spluque@gmail.com>"
 __license__ = "AGPLv3"
-__version__ = "0.4.0"
+__version__ = "1.0.0"
 __all__ = ["TDR", "calibrate", "dump_config_template"]

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/bouts/bouts.py

@@ -189,6 +189,7 @@ def _plot_bec(bec_x, bec_y, ax, xytext, horizontalalignment="left"):
     fmtstr = "bec_{0} = {1:.3f}"
     if bec_x.size == 1:
         bec_x = bec_x.item()
+        bec_y = bec_y.item()
         ax.annotate(fmtstr.format(0, bec_x),
                     (bec_x, bec_y), xytext=xytext,
                     textcoords="offset points",

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/calibspeed.py

@@ -18,8 +18,7 @@ logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 
 
-def calibrate_speed(x, tau, contour_level, z=0, bad=[0, 0],
-                    plot=True, ax=None):
+def calibrate_speed(x, tau, contour_level, plot=True, ax=None):
     """Calibration based on kernel density estimation
 
     Parameters
@@ -28,8 +27,6 @@ def calibrate_speed(x, tau, contour_level, z=0, bad=[0, 0],
         DataFrame with depth rate and speed
     tau : float
     contour_level : float
-    z : float, optional
-    bad : array_like, optional
     plot : bool, optional
         Whether to plot calibration results.
     ax : matplotlib.Axes, optional

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/plotting.py

@@ -33,8 +33,8 @@ def _night(times, sunrise_time, sunset_time):
     sunsets = pd.date_range(start=tmin + sunset_time,
                             end=tmax + sunset_time,
                             freq="1D")
-    tmin1 = (times.min() + pd.Timedelta(1, unit="d")).strftime("%Y-%m-%d ")
-    tmax1 = (times.max() + pd.Timedelta(1, unit="d")).strftime("%Y-%m-%d ")
+    tmin1 = (times.min() + pd.Timedelta(1, unit="D")).strftime("%Y-%m-%d ")
+    tmax1 = (times.max() + pd.Timedelta(1, unit="D")).strftime("%Y-%m-%d ")
     sunrises = pd.date_range(start=tmin1 + sunrise_time,
                              end=tmax1 + sunrise_time,
                              freq="1D")

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/tdr.py

@@ -150,7 +150,7 @@ class TDR(TDRPhases):
                               curspeed), axis=1)
         qfit, ax = speedcal.calibrate_speed(kde_data, tau=tau,
                                             contour_level=contour_level,
-                                            z=z, bad=bad, **kwargs)
+                                            **kwargs)
         self.speed_calib_fit = qfit
         logger.info("Finished calibrating speed")
 

{scikit_divemove-0.4.0 → scikit_divemove-1.0.0}/skdiveMove/tests/get_sample_data.py

@@ -7,7 +7,6 @@ from skdiveMove.tdr import TDR
 from skdiveMove.tdrsource import TDRSource
 from skdiveMove.tdrphases import TDRPhases
 from skdiveMove.zoc import ZOC
-from skdiveMove.imutools import IMU2Body
 
 
 def diveMove2skd(oclass="TDR", **kwargs):
@@ -44,18 +43,3 @@ def diveMove2skd(oclass="TDR", **kwargs):
                            .format(oclass)))
 
     return tdrX
-
-
-def _nc2imu2body():
-    """Get example data into a IMU2Body instance
-
-    Convenience function for tests and examples.
-
-    """
-    ncfname = "gert_imu_frame.nc"
-    icdf = (rsrc.files("skdiveMove") / "tests" /
-            "data" / "gertrude" / ncfname)
-    icsv = (rsrc.files("skdiveMove") / "tests" /
-            "data" / "gertrude" / "gert_long_srfc.csv")
-
-    return IMU2Body.from_csv_nc(icsv, icdf, imu_filename=ncfname)

scikit_divemove-0.4.0/MANIFEST.in

@@ -1,2 +0,0 @@
-recursive-include skdiveMove/tests/data *.db *.txt *.csv *.nc
-recursive-include skdiveMove/config_examples *.json