Merge branch 'main' into feat-add-logger

# Conflicts:
#	src/icesat2waves/app.py

README.md

@@ -9,7 +9,7 @@
 
 Prerequisites:
 - A POSIX-compatible system (Linux or macOS)
-- Python 3.9 (run `python --version` to check that your version of python is correct)
+- Python 3.10 (run `python --version` to check that your version of python is correct)
 - MPI (e.g. from `brew install open-mpi` on macOS)
 - HDF5 (e.g. from `brew install hdf5` on macOS)
 
@@ -55,9 +55,9 @@ Installation:
   > pip install --upgrade --editable ".[dev]"
   > ```
 
-- Check the module `icesat2_tracks` is available by loading the module:
+- Check the module `icesat2waves` is available by loading the module:
   ```shell
-  python -c "import icesat2_tracks; print(icesat2_tracks.__version__)"
+  python -c "import icesat2waves; print(icesat2waves.__version__)"
   ```
 
 ## Command line interface

pyproject.toml

@@ -10,7 +10,7 @@
 # There are some restrictions on what makes a valid project name
 # specification here:
 # https://packaging.python.org/specifications/core-metadata/#name
-name = "icesat2-tracks"  # Required
+name = "icesat2waves"  # Required
 
 # Versions should comply with PEP 440:
 # https://www.python.org/dev/peps/pep-0440/
@@ -39,7 +39,7 @@ readme = "README.md" # Optional
 # 'Programming Language' classifiers above, 'pip install' will check this
 # and refuse to install the project if the version does not match. See
 # https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 # This is either text indicating the license for the distribution, or a file
 # that contains the license
@@ -92,7 +92,6 @@ classifiers = [  # Optional
   # Specify the Python versions you support here. In particular, ensure
   # that you indicate you support Python 3. These classifiers are *not*
   # checked by "pip install". See instead "python_requires" below.
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3 :: Only",
@@ -140,7 +139,7 @@ dependencies = [ # Optional
 dev = [
   "check-manifest",
   "black",
-  "icesat2-tracks[test]"
+  "icesat2waves[test]"
 ]
 test = [
   "coverage",
@@ -159,22 +158,22 @@ test = [
 # maintainers, and where to support the project financially. The key is
 # what's used to render the link text on PyPI.
 [project.urls]  # Optional
-"Homepage" = "https://github.com/brown-ccv/icesat2-tracks"
-"Bug Reports" = "https://github.com/brown-ccv/icesat2-tracks/issues"
-"Source" = "https://github.com/brown-ccv/icesat2-tracks"
+"Homepage" = "https://github.com/brown-ccv/icesat2waves"
+"Bug Reports" = "https://github.com/brown-ccv/icesat2waves/issues"
+"Source" = "https://github.com/brown-ccv/icesat2waves"
 
 # The following would provide a command line executable called `sample`
 # which executes the function `main` from this package when invoked.
 [project.scripts]  # Optional
 #TODO: ADD ANY SCRIPTS WE WANT TO HAVE
-load-file = "icesat2_tracks.analysis_db.B01_SL_load_single_file:load_file_app"
-make-spectra = "icesat2_tracks.analysis_db.B02_make_spectra_gFT:make_spectra_app"
-plot-spectra = "icesat2_tracks.analysis_db.B03_plot_spectra_ov:plot_spectra"
-make-iowaga-threads-prior = "icesat2_tracks.analysis_db.A02c_IOWAGA_thredds_prior:make_iowaga_threads_prior_app"
-make-b04-angle = "icesat2_tracks.analysis_db.B04_angle:make_b04_angle_app"
-define-angle = "icesat2_tracks.analysis_db.B05_define_angle:define_angle_app"
-correct-separate = "icesat2_tracks.analysis_db.B06_correct_separate_var:correct_separate_app"
-icesat2waves = "icesat2_tracks.app:app"
+load-file = "icesat2waves.analysis_db.B01_SL_load_single_file:load_file_app"
+make-spectra = "icesat2waves.analysis_db.B02_make_spectra_gFT:make_spectra_app"
+plot-spectra = "icesat2waves.analysis_db.B03_plot_spectra_ov:plot_spectra"
+make-iowaga-threads-prior = "icesat2waves.analysis_db.A02c_IOWAGA_thredds_prior:make_iowaga_threads_prior_app"
+make-b04-angle = "icesat2waves.analysis_db.B04_angle:make_b04_angle_app"
+define-angle = "icesat2waves.analysis_db.B05_define_angle:define_angle_app"
+correct-separate = "icesat2waves.analysis_db.B06_correct_separate_var:correct_separate_app"
+icesat2waves = "icesat2waves.app:app"
 
 
 # This is configuration specific to the `setuptools` build backend.
@@ -183,7 +182,7 @@ icesat2waves = "icesat2_tracks.app:app"
 # If there are data files included in your packages that need to be
 # installed, specify them here.
 # TODO: ADD ANY DATA FILES WE WANT TO HAVE
-package-data = {"icesat2_tracks" = ["config/*.json"]}
+package-data = {"icesat2waves" = ["config/*.json"]}
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -196,4 +195,4 @@ where = ["src"]
 requires = ["setuptools>=43.0.0", "setuptools_scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
+[tool.setuptools_scm]

src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py → src/icesat2waves/analysis_db/A02c_IOWAGA_thredds_prior.py

@@ -13,15 +13,15 @@
 from siphon.catalog import TDSCatalog
 import typer
 
-from icesat2_tracks.config.IceSAT2_startup import mconfig
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
-import icesat2_tracks.ICEsat2_SI_tools.wave_tools as waves
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-import icesat2_tracks.local_modules.m_general_ph3 as M
-from icesat2_tracks.config.IceSAT2_startup import color_schemes
-from icesat2_tracks.config.IceSAT2_startup import font_for_print
-
-from icesat2_tracks.clitools import (
+from icesat2waves.config.startup import mconfig
+import icesat2waves.tools.iotools as io
+import icesat2waves.tools.wave_tools as waves
+import icesat2waves.local_modules.m_tools_ph3 as MT
+import icesat2waves.local_modules.m_general_ph3 as M
+from icesat2waves.config.startup import color_schemes
+from icesat2waves.config.startup import font_for_print
+
+from icesat2waves.clitools import (
     echo,
     validate_batch_key,
     validate_output_dir,

src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py → src/icesat2waves/analysis_db/B01_SL_load_single_file.py

@@ -17,19 +17,19 @@
     SettingWithCopyWarning,
 )  # TODO: remove when warnings are handled
 
-from icesat2_tracks.config.IceSAT2_startup import (
+from icesat2waves.config.startup import (
     mconfig,
     color_schemes,
     font_for_pres,
     plt,
 )
-import icesat2_tracks.ICEsat2_SI_tools.sliderule_converter_tools as sct
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
-import icesat2_tracks.ICEsat2_SI_tools.beam_stats as beam_stats
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-from icesat2_tracks.local_modules import m_general_ph3 as M
+import icesat2waves.tools.sliderule_converter_tools as sct
+import icesat2waves.tools.iotools as io
+import icesat2waves.tools.beam_stats as beam_stats
+import icesat2waves.local_modules.m_tools_ph3 as MT
+from icesat2waves.local_modules import m_general_ph3 as M
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     validate_track_name,
     validate_batch_key,
     validate_output_dir,

src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py → src/icesat2waves/analysis_db/B02_make_spectra_gFT.py

@@ -20,15 +20,15 @@
 from matplotlib import pyplot as plt
 import typer
 
-import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
-import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec
-import icesat2_tracks.local_modules.m_general_ph3 as M
-import icesat2_tracks.local_modules.m_spectrum_ph3 as spicke_remover
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-from icesat2_tracks.config.IceSAT2_startup import mconfig
-
-from icesat2_tracks.clitools import (
+import icesat2waves.tools.generalized_FT as gFT
+import icesat2waves.tools.iotools as io
+import icesat2waves.tools.spectral_estimates as spec
+import icesat2waves.local_modules.m_general_ph3 as M
+import icesat2waves.local_modules.m_spectrum_ph3 as spicke_remover
+import icesat2waves.local_modules.m_tools_ph3 as MT
+from icesat2waves.config.startup import mconfig
+
+from icesat2waves.clitools import (
     echo,
     validate_batch_key,
     validate_output_dir,

src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py → src/icesat2waves/analysis_db/B03_plot_spectra_ov.py

@@ -11,18 +11,18 @@
 from matplotlib.gridspec import GridSpec
 import typer
 
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
-import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-from icesat2_tracks.local_modules import m_general_ph3 as M
-from icesat2_tracks.config.IceSAT2_startup import (
+import icesat2waves.tools.iotools as io
+import icesat2waves.tools.generalized_FT as gFT
+import icesat2waves.local_modules.m_tools_ph3 as MT
+from icesat2waves.local_modules import m_general_ph3 as M
+from icesat2waves.config.startup import (
     mconfig,
     color_schemes,
     plt,
     font_for_print,
 )
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     echo,
     validate_batch_key,
     validate_output_dir,

src/icesat2_tracks/analysis_db/B04_angle.py → src/icesat2waves/analysis_db/B04_angle.py

@@ -6,7 +6,7 @@
 
 import itertools
 
-from icesat2_tracks.config.IceSAT2_startup import (
+from icesat2waves.config.startup import (
     mconfig,
     color_schemes,
     font_for_print,
@@ -15,7 +15,7 @@
 
 
 import h5py
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
+import icesat2waves.tools.iotools as io
 import xarray as xr
 import numpy as np
 from scipy.constants import g
@@ -25,11 +25,11 @@
 import matplotlib.pyplot as plt
 from numba import jit  # maybe for later optimizations?  # noqa: F401
 
-from icesat2_tracks.ICEsat2_SI_tools import angle_optimizer
+from icesat2waves.tools import angle_optimizer
 
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-import icesat2_tracks.local_modules.m_general_ph3 as M
-from icesat2_tracks.ICEsat2_SI_tools import angle_optimizer
+import icesat2waves.local_modules.m_tools_ph3 as MT
+import icesat2waves.local_modules.m_general_ph3 as M
+from icesat2waves.tools import angle_optimizer
 
 import pandas as pd
 
@@ -38,7 +38,7 @@
 
 from typer import Option
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     validate_batch_key,
     validate_output_dir,
     suppress_stdout,

src/icesat2_tracks/analysis_db/B05_define_angle.py → src/icesat2waves/analysis_db/B05_define_angle.py

@@ -9,26 +9,26 @@
 from matplotlib import pyplot as plt
 from typer import Option
 
-from icesat2_tracks.config.IceSAT2_startup import (
+from icesat2waves.config.startup import (
     mconfig,
     color_schemes,
     font_for_print,
 )
 
-from icesat2_tracks.ICEsat2_SI_tools.iotools import init_from_input, ID_to_str
-import icesat2_tracks.ICEsat2_SI_tools.spectral_estimates as spec
+from icesat2waves.tools.iotools import init_from_input, ID_to_str
+import icesat2waves.tools.spectral_estimates as spec
 
 import xarray as xr
 import numpy as np
 import time
-import icesat2_tracks.ICEsat2_SI_tools.lanczos as lanczos
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-import icesat2_tracks.local_modules.m_general_ph3 as M
+import icesat2waves.tools.lanczos as lanczos
+import icesat2waves.local_modules.m_tools_ph3 as MT
+import icesat2waves.local_modules.m_general_ph3 as M
 
 from matplotlib.gridspec import GridSpec
 from scipy.ndimage import label
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     validate_batch_key,
     validate_output_dir,
     suppress_stdout,

src/icesat2_tracks/analysis_db/B06_correct_separate_var.py → src/icesat2waves/analysis_db/B06_correct_separate_var.py

@@ -8,12 +8,12 @@
 
 import h5py
 from pathlib import Path
-import icesat2_tracks.ICEsat2_SI_tools.iotools as io
-import icesat2_tracks.local_modules.m_tools_ph3 as MT
-from icesat2_tracks.local_modules import m_general_ph3 as M
+import icesat2waves.tools.iotools as io
+import icesat2waves.local_modules.m_tools_ph3 as MT
+from icesat2waves.local_modules import m_general_ph3 as M
 import time
 import copy
-import icesat2_tracks.ICEsat2_SI_tools.generalized_FT as gFT
+import icesat2waves.tools.generalized_FT as gFT
 import pandas as pd
 import xarray as xr
 import numpy as np
@@ -22,7 +22,7 @@
 import piecewise_regression
 import typer
 
-from icesat2_tracks.config.IceSAT2_startup import (
+from icesat2waves.config.startup import (
     mconfig,
     color_schemes,
     font_for_pres,
@@ -31,7 +31,7 @@
     fig_sizes,
 )
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     echo,
     validate_batch_key,
     validate_output_dir,

src/icesat2_tracks/app.py → src/icesat2waves/app.py

@@ -8,33 +8,33 @@
 from typer import Typer, Option
 from typing_extensions import Annotated
 
-from icesat2_tracks.analysis_db.B01_SL_load_single_file import (
+from icesat2waves.analysis_db.B01_SL_load_single_file import (
     run_B01_SL_load_single_file as _loadfile,
 )
 
-from icesat2_tracks.analysis_db.B02_make_spectra_gFT import (
+from icesat2waves.analysis_db.B02_make_spectra_gFT import (
     run_B02_make_spectra_gFT as _makespectra,
 )
 
-from icesat2_tracks.analysis_db.B03_plot_spectra_ov import (
+from icesat2waves.analysis_db.B03_plot_spectra_ov import (
     run_B03_plot_spectra_ov as _plotspectra,
 )
 
-from icesat2_tracks.analysis_db.A02c_IOWAGA_thredds_prior import (
+from icesat2waves.analysis_db.A02c_IOWAGA_thredds_prior import (
     run_A02c_IOWAGA_thredds_prior as _threddsprior,
 )
 
 
-from icesat2_tracks.analysis_db.B04_angle import run_B04_angle as _run_B04_angle
+from icesat2waves.analysis_db.B04_angle import run_B04_angle as _run_B04_angle
 
-from icesat2_tracks.analysis_db.B05_define_angle import define_angle as _define_angle
+from icesat2waves.analysis_db.B05_define_angle import define_angle as _define_angle
 
-from icesat2_tracks.analysis_db.B06_correct_separate_var import (
+from icesat2waves.analysis_db.B06_correct_separate_var import (
     run_B06_correct_separate_var as _run_correct_separate_var,
 )
 
 
-from icesat2_tracks.clitools import (
+from icesat2waves.clitools import (
     validate_track_name,
     validate_batch_key,
     validate_output_dir,
@@ -60,8 +60,8 @@ def level(self):
             _LogLevel.VERBOSE: logging.INFO,
             _LogLevel.DEBUG: logging.DEBUG,
         }[self.value]
- 
-       
+
+
 @app.callback()
 def main(
     log: Annotated[

src/icesat2_tracks/config/generate_colors.py → src/icesat2waves/config/generate_colors.py

@@ -1,5 +1,5 @@
 #%matplotlib inline
-from icesat2_tracks.local_modules import m_colormanager_ph3 as M_color
+from icesat2waves.local_modules import m_colormanager_ph3 as M_color
 
 mconfig['paths']
 path=mconfig['paths']['config']

src/icesat2_tracks/config/IceSAT2_startup.py → src/icesat2waves/config/startup.py

@@ -4,8 +4,8 @@
 
 import matplotlib.pyplot as plt
 
-from icesat2_tracks.local_modules import m_colormanager_ph3 as M_color
-from icesat2_tracks.local_modules import m_tools_ph3 as MT
+from icesat2waves.local_modules import m_colormanager_ph3 as M_color
+from icesat2waves.local_modules import m_tools_ph3 as MT
 
 ## Read folders and configuration paths
 config_dir_path = os.path.dirname(__file__)

src/icesat2_tracks/local_modules/m_spectrum_ph3.py → src/icesat2waves/local_modules/m_spectrum_ph3.py

@@ -4,7 +4,7 @@
 from scipy.special import gammainc
 from scipy import signal
 import matplotlib.pyplot as plt
-from icesat2_tracks.local_modules import m_general_ph3 as M
+from icesat2waves.local_modules import m_general_ph3 as M
 
 try:
     import mkl