s1_reader.py: implement load_bursts speedups (#75)

* s1_reader.py: implement load_bursts speedups

the three speedups are

1. use fromisoformat instead of strptime

2. use lxml to parse if available

3. use eval poly1d by passing array instead of a comprehension

* remove unused fmt arg, fix existing typos

* make lxml part of requirements

* update circlci deps with docker

Author: scottstanie

.circleci/freeze-deps.sh

@@ -2,5 +2,5 @@
 docker run -v "$PWD:/mnt" -w /mnt --rm -it continuumio/miniconda3 bash -c '\
     conda config --add channels conda-forge && \
     conda config --remove channels defaults && \
-    conda update conda && \
-    conda install -y -c conda-forge isce3=0.8 build setuptools pytest isce3 shapely && conda list --explicit > specfile.txt'
+    conda update -y conda && \
+    conda install -y -c conda-forge isce3=0.8 build setuptools pytest isce3 shapely lxml && conda list --explicit > specfile.txt'

.circleci/specfile.txt

@@ -3,52 +3,53 @@
 # platform: linux-64
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-https://conda.anaconda.org/conda-forge/linux-64/tzcode-2022c-h166bdaf_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/tzcode-2022e-h166bdaf_0.tar.bz2
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@@ -58,104 +59,105 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h7f98852_10
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-https://conda.anaconda.org/conda-forge/linux-64/pep517-0.12.0-py39hf3d152e_2.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/pluggy-1.0.0-py39hf3d152e_3.tar.bz2
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-https://conda.anaconda.org/conda-forge/linux-64/pycosat-0.6.3-py39hb9d737c_1010.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/pep517-0.12.0-pyhd8ed1ab_3.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/pip-22.3-pyhd8ed1ab_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/pluggy-1.0.0-py39hf3d152e_4.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/poppler-22.10.0-h92391eb_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/pycosat-0.6.4-py39hb9d737c_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/pyre-1.11.2-py39h8b9aba8_2.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/pysocks-1.7.1-py39hf3d152e_5.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0-py39hb9d737c_4.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0-py39hb9d737c_5.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.6-py39hb9d737c_1.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/ruamel_yaml-0.15.80-py39hb9d737c_1007.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/setuptools-65.3.0-py39hf3d152e_0.tar.bz2
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-https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py39hb9d737c_1004.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/tiledb-2.11.3-h3f4058f_1.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/tqdm-4.64.1-pyhd8ed1ab_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py39hb9d737c_1005.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/build-0.7.0-pyhd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/conda-package-handling-1.8.1-py39hb9d737c_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/linux-64/cryptography-36.0.0-py39h9ce1e76_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/conda-package-handling-1.9.0-py39hb9d737c_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/cryptography-38.0.2-py39h3ccb8fc_1.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/h5py-3.7.0-nompi_py39hd51670d_101.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/libgdal-3.5.1-h84f2e82_5.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/pip-22.2.2-pyhd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/pytest-7.1.2-py39hf3d152e_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgdal-3.5.2-h27ae5c1_5.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/pytest-7.2.0-py39hf3d152e_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.17.21-py39hb9d737c_1.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/scipy-1.9.0-py39h8ba3f38_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/shapely-1.8.4-py39h68ae834_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.9.3-py39hddc5342_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/shapely-1.8.5-py39h5b5020f_0.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/yamale-4.0.4-pyh6c4a22f_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/gdal-3.5.1-py39h5e8c895_5.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/gdal-3.5.2-py39h5cb30a4_5.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.1.0-pyhd8ed1ab_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/isce3-0.8.0-py39h6f86a94_1.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.11-pyhd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/conda-4.14.0-py39hf3d152e_0.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/conda-22.9.0-py39hf3d152e_1.tar.bz2

.gitignore

@@ -116,6 +116,9 @@ venv.bak/
 .spyderproject
 .spyproject
 
+# VScode project settings
+.vscode
+
 # Rope project settings
 .ropeproject
 

requirements.txt

@@ -5,3 +5,4 @@ packaging
 requests
 #isce3    # since the conda-installed isce3 is not the most updated version, installing isce3 from stratch is recommended, to stay in sync with isce3 development.
 shapely
+lxml

src/s1reader/s1_annotation.py

@@ -7,7 +7,7 @@
 
 import datetime
 import os
-import xml.etree.ElementTree as ET
+import lxml.etree as ET
 import zipfile
 
 import numpy as np