[Git][debian-gis-team/pysolid][upstream] New upstream version 0.3.1
Antonio Valentino (@antonio.valentino)
gitlab at salsa.debian.org
Mon Aug 21 21:36:27 BST 2023
Antonio Valentino pushed to branch upstream at Debian GIS Project / pysolid
Commits:
bf234de6 by Antonio Valentino at 2023-08-21T20:23:29+00:00
New upstream version 0.3.1
- - - - -
15 changed files:
- .circleci/config.yml
- .github/workflows/build-and-publish-to-pypi.yml
- README.md
- + docs/images/set_grid.png
- + docs/images/set_point_psd.png
- docs/logo.pptx → docs/images/set_point_ts.png
- + docs/requirements.txt
- − environment.yml
- pyproject.toml
- requirements.txt
- setup.py
- src/pysolid/grid.py
- src/pysolid/point.py
- src/pysolid/solid.for
- + tests/requirements.txt
Changes:
=====================================
.circleci/config.yml
=====================================
@@ -25,43 +25,40 @@ jobs:
docker:
- image: ubuntu:bionic
environment:
- CONDA_PREFIX: /root/tools/miniconda3
+ CONDA_PREFIX: /root/tools/mambaforge
+ PYSOLID_HOME: /root/tools/PySolid
user: root
working_directory: /root/tools/PySolid
# Checkout the code as the first step. This is a dedicated CircleCI step.
steps:
- checkout
- run:
- name: Setting Environment with Miniconda
+ name: Setting Environment with Mambaforge
command: |
apt update
apt-get update --yes && apt-get upgrade --yes
apt-get install --yes wget git
- # download and install miniconda3
+ # download and install mambaforge
mkdir -p ${HOME}/tools
cd ${HOME}/tools
- wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
- bash Miniconda3-latest-Linux-x86_64.sh -b -p ${HOME}/tools/miniconda3
- ${HOME}/tools/miniconda3/bin/conda init bash
- ${HOME}/tools/miniconda3/bin/conda config --add channels conda-forge
- ${HOME}/tools/miniconda3/bin/conda install -c conda-forge --yes mamba
+ wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+ bash Mambaforge-Linux-x86_64.sh -b -p ${HOME}/tools/mambaforge
+ ${HOME}/tools/mambaforge/bin/mamba init bash
+ # modify/export env var PATH to BASH_ENV to be shared across run steps
+ echo 'export PATH=${CONDA_PREFIX}/bin:${PATH}' >> ${BASH_ENV}
+
- run:
name: Installing PySolid
no_output_timeout: 10m
command: |
export PYTHONUNBUFFERED=1
- # setup environment variable
- export PATH=${CONDA_PREFIX}/bin:${PATH}
- # install dependencies
- source activate root
- mamba install --verbose --yes fortran-compiler --file ${HOME}/tools/PySolid/requirements.txt
- python -m pip install ${HOME}/tools/PySolid
+ # install dependencies and source code
+ mamba install --verbose --yes fortran-compiler --file ${PYSOLID_HOME}/requirements.txt --file ${PYSOLID_HOME}/tests/requirements.txt
+ python -m pip install ${PYSOLID_HOME}
- run:
- name: Test
+ name: Unit Test
command: |
- # setup environment variables
- export PATH=${CONDA_PREFIX}/bin:${PATH}
# run tests
- python ${HOME}/tools/PySolid/tests/point.py
- python ${HOME}/tools/PySolid/tests/grid.py
+ python ${PYSOLID_HOME}/tests/point.py
+ python ${PYSOLID_HOME}/tests/grid.py
=====================================
.github/workflows/build-and-publish-to-pypi.yml
=====================================
@@ -43,7 +43,7 @@ jobs:
echo "[build]`ncompiler=mingw32" | Out-File -Encoding ASCII ~/pydistutils.cfg
- name: Build wheels
- uses: pypa/cibuildwheel at v2.12.1
+ uses: pypa/cibuildwheel at v2.14.1
env:
# Disable building for PyPy and 32bit.
CIBW_SKIP: pp* *-win32 *-manylinux_i686
=====================================
README.md
=====================================
@@ -1,8 +1,8 @@
[](https://www.python.org/)
-[](https://circleci.com/gh/insarlab/PySolid)
-[](https://github.com/insarlab/PySolid/releases)
-[](https://anaconda.org/conda-forge/pysolid)
-[](https://github.com/insarlab/PySolid/blob/main/LICENSE)
+[](https://circleci.com/gh/insarlab/PySolid)
+[](https://anaconda.org/conda-forge/pysolid)
+[](https://github.com/insarlab/PySolid/releases)
+[](https://github.com/insarlab/PySolid/blob/main/LICENSE)
[](https://doi.org/10.1109/TGRS.2022.3168509)
## PySolid
@@ -42,14 +42,14 @@ git clone https://github.com/insarlab/PySolid.git
```bash
# option 1: use conda to install dependencies into an existing, activated environment
-conda install -c conda-forge fortran-compiler --file PySolid/requirements.txt
+conda install -c conda-forge fortran-compiler --file PySolid/requirements.txt --file PySolid/tests/requirements.txt
-# option 2: use conda to create a new environment named "pysolid"
-conda env create -f PySolid/environment.yml
+# option 2: use conda to install dependencies into a new environment, e.g. named "pysolid"
+conda create --name pysolid fortran-compiler --file PySolid/requirements.txt --file PySolid/tests/requirements.txt
conda activate pysolid
# option 3: have a Fortran compiler already installed and use pip to install the rest dependencies
-python -m pip install -r PySolid/requirements.txt
+python -m pip install -r PySolid/requirements.txt -r PySolid/tests/requirements.txt
```
##### c. Install PySolid
@@ -112,8 +112,8 @@ pysolid.plot_power_spectral_density4tides(tide_u, sample_spacing=step_sec)
```
<p align="left">
- <img width="600" src="https://yunjunzhang.files.wordpress.com/2021/01/set_ts_up-1.png">
- <img width="600" src="https://yunjunzhang.files.wordpress.com/2021/01/set_psd-1.png">
+ <img width="600" src="./docs/images/set_point_ts.png">
+ <img width="600" src="./docs/images/set_point_psd.png">
</p>
#### 2.2 Grid Mode [[notebook](./docs/plot_grid_SET.ipynb)]
@@ -152,10 +152,10 @@ tide_los = ( tide_e * np.sin(inc_angle) * np.sin(az_angle) * -1
```
<p align="left">
- <img width="800" src="https://yunjunzhang.files.wordpress.com/2021/01/set_grid-3.png">
+ <img width="800" src="./docs/images/set_grid.png">
</p>
### 3. Citing this work
-+ Yunjun, Z., Fattahi, H., Pi, X., Rosen, P., Simons, M., Agram, P., & Aoki, Y. (2022). Range Geolocation Accuracy of C-/L-band SAR and its Implications for Operational Stack Coregistration. _IEEE Trans. Geosci. Remote Sens., 60_, 1-19, doi:[10.1109/TGRS.2022.3168509](https://doi.org/10.1109/TGRS.2022.3168509), [arXiv](https://doi.org/10.31223/X5F641), [data](https://zenodo.org/record/6360749), [notebooks](https://github.com/yunjunz/2022-Geolocation).
++ Yunjun, Z., Fattahi, H., Pi, X., Rosen, P., Simons, M., Agram, P., & Aoki, Y. (2022). Range Geolocation Accuracy of C-/L-band SAR and its Implications for Operational Stack Coregistration. _IEEE Trans. Geosci. Remote Sens., 60_, 5227219. [ [doi](https://doi.org/10.1109/TGRS.2022.3168509) \| [arxiv](https://doi.org/10.31223/X5F641) \| [data](https://doi.org/10.5281/zenodo.6360749) \| [notebook](https://github.com/yunjunz/2022-Geolocation) ]
+ Milbert, D. (2018), "solid: Solid Earth Tide", [Online]. Available: http://geodesyworld.github.io/SOFTS/solid.htm. Accessd on: 2020-09-06.
=====================================
docs/images/set_grid.png
=====================================
Binary files /dev/null and b/docs/images/set_grid.png differ
=====================================
docs/images/set_point_psd.png
=====================================
Binary files /dev/null and b/docs/images/set_point_psd.png differ
=====================================
docs/logo.pptx → docs/images/set_point_ts.png
=====================================
Binary files a/docs/logo.pptx and b/docs/images/set_point_ts.png differ
=====================================
docs/requirements.txt
=====================================
@@ -0,0 +1,4 @@
+# extra dependencies required for running notebooks
+cartopy
+matplotlib
+mintpy
=====================================
environment.yml deleted
=====================================
@@ -1,17 +0,0 @@
-name: pysolid
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python>=3.8
- # for running
- - numpy
- - scipy
- - matplotlib
- - scikit-image
- # for packaging and installation
- - fortran-compiler # Fortran compiler across platforms through conda-forge channel
- - pip
- - setuptools
- - setuptools_scm
- - wheel
=====================================
pyproject.toml
=====================================
@@ -6,14 +6,14 @@ build-backend = "setuptools.build_meta"
name = "pysolid"
description = "A Python wrapper for solid to compute solid Earth tides"
authors = [
- {name="Zhang Yunjun", email="yunjunzgeo at gmail.com"},
+ {name="Zhang Yunjun", email="yunjunz at outlook.com"},
{name="Dennis Milbert"},
]
readme = "README.md"
requires-python = ">=3.8"
keywords = ["solid Earth tides", "deformation", "geodesy", "geophysics"]
license = {text = "GPL-3.0-or-later"}
-classifiers=[
+classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
@@ -21,13 +21,11 @@ classifiers=[
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
]
-dependencies = [
- "numpy",
- "scipy",
- "matplotlib",
- "scikit-image",
-]
-dynamic = ["version"]
+
+# see section: setuptools_scm
+# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#dynamic-metadata
+# dependencies will be read from text files
+dynamic = ["version", "dependencies", "optional-dependencies"]
[project.urls]
"Homepage" = "https://github.com/insarlab/PySolid"
@@ -37,6 +35,16 @@ dynamic = ["version"]
include-package-data = true
zip-safe = false
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }
+
+# extra requirements: `pip install pysolid[docs]` or `pip install .[docs,test]`
+# note: the [docs] syntax requires setuptools>=64.0, thus, not working yet.
+[tool.setuptools.dynamic.optional-dependencies.docs]
+file = ["docs/requirements.txt"]
+[tool.setuptools.dynamic.optional-dependencies.test]
+file = ["tests/requirements.txt"]
+
[tool.setuptools.packages.find]
where = ["src"]
=====================================
requirements.txt
=====================================
@@ -1,8 +1,6 @@
# for running
numpy
scipy
-matplotlib
-scikit-image
# for packaging and installation
#fortran-compiler # Fortran compiler across platforms through conda-forge channel
pip
=====================================
setup.py
=====================================
@@ -18,7 +18,7 @@ setup(
long_description=readme(),
long_description_content_type="text/markdown",
author="Zhang Yunjun, Dennis Milbert",
- author_email="yunjunzgeo at gmail.com",
+ author_email="yunjunz at outlook.com",
license="GPL-3.0-or-later",
license_files=("LICENSE",),
@@ -42,8 +42,6 @@ setup(
install_requires=[
"numpy",
"scipy",
- "matplotlib",
- "scikit-image",
],
# package discovery
=====================================
src/pysolid/grid.py
=====================================
@@ -14,7 +14,7 @@
import os
import numpy as np
-from skimage.transform import resize
+from scipy import ndimage
################################## Earth tides - grid mode ###################################
@@ -79,13 +79,16 @@ def calc_solid_earth_tides_grid(dt_obj, atr, step_size=1e3, display=False, verbo
lon0, lon_step, width)
# resample to the input size
+ # via scipy.ndimage.zoom or skimage.transform.resize
if num_step > 1:
+ in_shape = tide_e.shape
out_shape = (int(atr['LENGTH']), int(atr['WIDTH']))
vprint('PYSOLID: resize data to the shape of {} using order-1 spline interpolation'.format(out_shape))
- kwargs = dict(order=1, mode='edge', anti_aliasing=True, preserve_range=True)
- tide_e = resize(tide_e, out_shape, **kwargs)
- tide_n = resize(tide_n, out_shape, **kwargs)
- tide_u = resize(tide_u, out_shape, **kwargs)
+
+ enu = np.stack([tide_e, tide_n, tide_u])
+ zoom_factors = [1, *np.divide(out_shape, in_shape)]
+ kwargs = dict(order=1, mode="nearest", grid_mode=True)
+ tide_e, tide_n, tide_u = ndimage.zoom(enu, zoom_factors, **kwargs)
# plot
if display:
=====================================
src/pysolid/point.py
=====================================
@@ -16,8 +16,6 @@ import datetime as dt
import os
import numpy as np
-from matplotlib import pyplot as plt, ticker, dates as mdates
-from scipy import signal
## Tidal constituents
@@ -94,10 +92,10 @@ def calc_solid_earth_tides_point(lat, lon, dt0, dt1, step_sec=60, display=False,
"""
print('PYSOLID: calculate solid Earth tides in east/north/up direction')
- print('PYSOLID: lot/lon: {}/{} degree'.format(lat, lon))
- print('PYSOLID: start UTC: {}'.format(dt0.isoformat()))
- print('PYSOLID: end UTC: {}'.format(dt1.isoformat()))
- print('PYSOLID: time step: {} seconds'.format(step_sec))
+ print(f'PYSOLID: lot/lon: {lat}/{lon} degree')
+ print(f'PYSOLID: start UTC: {dt0.isoformat()}')
+ print(f'PYSOLID: end UTC: {dt1.isoformat()}')
+ print(f'PYSOLID: time step: {step_sec} seconds')
dt_out = []
tide_e = []
@@ -108,7 +106,7 @@ def calc_solid_earth_tides_point(lat, lon, dt0, dt1, step_sec=60, display=False,
for i in range(ndays):
di = dt0.date() + dt.timedelta(days=i)
if verbose:
- print('SOLID : {} {}/{} ...'.format(di.isoformat(), i+1, ndays))
+ print(f'SOLID : {di.isoformat()} {i+1}/{ndays} ...')
# calc tide_u/n/u for the whole day
(dt_outi,
@@ -185,6 +183,8 @@ def calc_solid_earth_tides_point_per_day(lat, lon, date_str, step_sec=60):
def plot_solid_earth_tides_point(dt_out, tide_e, tide_n, tide_u, lalo=None,
out_fig=None, save=False, display=True):
"""Plot the solid Earth tides at one point."""
+ from matplotlib import pyplot as plt, dates as mdates
+
# plot
fig, axs = plt.subplots(nrows=3, ncols=1, figsize=[6, 4], sharex=True)
for ax, data, label in zip(axs.flatten(),
@@ -227,6 +227,9 @@ def plot_power_spectral_density4tides(tide_ts, sample_spacing, out_fig=None, fig
"""Plot the power spectral density (PSD) of tides time-series.
Note: for accurate PSD analysis, a long time-series, e.g. one year, is recommended.
"""
+ from matplotlib import pyplot as plt, ticker
+ from scipy import signal
+
## calc PSD
freq, psd = signal.periodogram(tide_ts, fs=1/sample_spacing, scaling='density')
# get rid of zero in the first element
=====================================
src/pysolid/solid.for
=====================================
@@ -1559,9 +1559,9 @@
implicit double precision(a-h,o-z)
double precision tsec
- !*** upper limit, leap second table, 2023dec28
+ !*** upper limit, leap second table, 2024jun28
!*** lower limit, leap second table, 1972jan01
- parameter(MJDUPPER=60306)
+ parameter(MJDUPPER=60489)
parameter(MJDLOWER=41317)
!*** leap second table limit flag
@@ -1642,7 +1642,7 @@
***** other leap second references at:
***** http://hpiers.obspm.fr/eoppc/bul/bulc/Leap_Second_History.dat
***** http://hpiers.obspm.fr/eoppc/bul/bulc/bulletinc.dat
-***** File expires on 28 December 2023
+***** File expires on 28 June 2024
*** test against newest leaps first
=====================================
tests/requirements.txt
=====================================
@@ -0,0 +1,2 @@
+# extra dependency required for testing
+matplotlib
View it on GitLab: https://salsa.debian.org/debian-gis-team/pysolid/-/commit/bf234de63766b1acef40bd8f69ccd399e411a7a5
--
View it on GitLab: https://salsa.debian.org/debian-gis-team/pysolid/-/commit/bf234de63766b1acef40bd8f69ccd399e411a7a5
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