wrap up for version 1.5.3 (#1120)

+ src/mintpy/version.py: add tag for version 1.5.3

+ simulation/fractal: fix np.abs(dtype) bug due to numpy behavior change

+ plot_network: fine-tune coh mat fig size for long time series

+ scripts/fix_typos.sh: use github.com instead of raw.githubusercontent.com for spelling.dat URL
   - use the github.com url for the spelling.dat file, as downloading raw.githubusercontent.com files in China does not work well
   - check gdal_dict.txt file instead of the ./fix_typos dir, so that one could run the script without deleting the ./fix_typos directory
   - add more words to the AUTHORIZED_LIST

+ fix some typos by running scripts/fix_typos.sh

+ docs/installation.md: add deprecation note for macports

Author: yunjunz

.gitignore

@@ -19,6 +19,7 @@ dist/
 downloads/
 eggs/
 .eggs/
+fix_typos/
 lib/
 lib64/
 parts/

docs/installation.md

@@ -19,7 +19,7 @@ mamba install -c conda-forge mintpy
 </details>
 
 <details>
-<p><summary>via docker</summary></p>
+<p><summary>or via docker</summary></p>
 
 Docker allows one to run MintPy in a dedicated container, which is essentially an efficient virtual machine, and to be independent of the platform OS. First, install <a href="https://docs.docker.com/install">docker</a> if you have not already done so. Then run the following to pull the latest stable released container image version from <a href="https://github.com/insarlab/MintPy/pkgs/container/mintpy">MintPy GitHub Container Registry</a> to your local machine:
 
@@ -31,7 +31,7 @@ docker pull ghcr.io/insarlab/mintpy:latest
 </details>
 
 <details>
-<p><summary>via apt (Linux Debian)</summary></p>
+<p><summary>or via apt (for Linux Debian)</summary></p>
 
 MintPy is available in the main archive of the <a href="https://tracker.debian.org/pkg/mintpy">Debian</a> GNU/Linux OS. It can be installed by using your favorite package manager or running the following command:
 
@@ -79,7 +79,6 @@ bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/tools/miniconda3
 Install the dependencies into a custom existing environment [recommended] by running:
 
 ```bash
-# To create a new custom environment, e.g. named "insar", run "conda create --name insar; conda activate insar"
 # To speedup, try "conda install mamba", then use "mamba install" to replace "conda install" below
 
 # Add "gdal'>=3'" below to install extra dependencies if you use ARIA, FRInGE, HyP3 or GMTSAR
@@ -89,13 +88,13 @@ conda install -c conda-forge --file ~/tools/MintPy/requirements.txt
 
 <p>
 <details>
-<p><summary>Or install the dependencies to a new environment, e.g. named "mintpy", by running:</summary></p>
+<p><summary>Or install the dependencies to a new environment, e.g. named "insar", by running:</summary></p>
 
 ```bash
 # Add "gdal'>=3'" below to install extra dependencies if you use ARIA, FRInGE, HyP3 or GMTSAR
 # Add "isce2"     below to install extra dependencies if you use ISCE-2
-conda create --name mintpy --file ~/tools/MintPy/requirements.txt
-conda activate mintpy
+conda create --name insar --file ~/tools/MintPy/requirements.txt
+conda activate insar
 ```
 </details>
 </p>
@@ -113,7 +112,7 @@ python -m pip install -e ~/tools/MintPy
 </details>
 
 <details>
-<p><summary>via path setup</summary></p>
+<p><summary>or via path setup</summary></p>
 
 Add below in your source file, e.g. <code>\~/.bash_profile</code> for <em>bash</em> users or <code>\~/.cshrc</code> for <em>csh/tcsh</em> users:
 
@@ -152,7 +151,7 @@ sudo xcodebuild -license</code></pre>
 <details>
 <p><summary>Or install MintPy via MacPorts</summary></p>
 
-Same as the instruction for Linux, except for the "b. Install dependencies" section, which is as below:
+Same as the instruction for Linux, except for the "b. Install dependencies" section, which is as below. Note that the installation procedure via MacPorts has not been maintained since Sep 2022, and will likely be phased out at some point, since conda/mamba works seamlessly on both MacOS and Linux.
 
 Install <a href="https://www.macports.org/install.php">macports</a> if you have not done so. Add the following at the bottom of your <code>~/.bash_profile</code> file:
 

scripts/fix_typos.sh

@@ -45,35 +45,39 @@ esac
 GDAL_ROOT=$SCRIPT_DIR/..
 cd "$GDAL_ROOT"
 
-if ! test -d fix_typos; then
+if [ ! -f fix_typos/gdal_dict.txt ]; then
     # Get our fork of codespell that adds --words-white-list and full filename support for -S option
-    mkdir fix_typos
-    (cd fix_typos
-     git clone https://github.com/rouault/codespell
-     (cd codespell && git checkout gdal_improvements)
-     # Aggregate base dictionary + QGIS one + Debian Lintian one
-     curl https://raw.githubusercontent.com/qgis/QGIS/master/scripts/spell_check/spelling.dat | sed "s/:/->/" | sed "s/:%//" | grep -v "colour->" | grep -v "colours->" > qgis.txt
-     curl https://salsa.debian.org/lintian/lintian/-/raw/master/data/spelling/corrections | grep "||" | grep -v "#" | sed "s/||/->/" > debian.txt
-     cat codespell/data/dictionary.txt qgis.txt debian.txt | awk 'NF' > gdal_dict.txt
-     echo "difered->deferred" >> gdal_dict.txt
-     echo "differed->deferred" >> gdal_dict.txt
-     grep -v 404 < gdal_dict.txt > gdal_dict.txt.tmp
-     mv gdal_dict.txt.tmp gdal_dict.txt
+    mkdir -p fix_typos
+    (
+        cd fix_typos
+        if [ ! -d codespell ]; then
+          git clone https://github.com/rouault/codespell
+        fi
+        (cd codespell && git checkout gdal_improvements)
+        # Aggregate base dictionary + QGIS one + Debian Lintian one
+        curl https://github.com/qgis/QGIS/blob/master/scripts/spell_check/spelling.dat | sed "s/:/->/" | sed "s/:%//" | grep -v "colour->" | grep -v "colours->" > qgis.txt
+        curl https://salsa.debian.org/lintian/lintian/-/raw/master/data/spelling/corrections | grep "||" | grep -v "#" | sed "s/||/->/" > debian.txt
+        cat codespell/data/dictionary.txt qgis.txt debian.txt | awk 'NF' > gdal_dict.txt
+        echo "difered->deferred" >> gdal_dict.txt
+        echo "differed->deferred" >> gdal_dict.txt
+        grep -v 404 < gdal_dict.txt > gdal_dict.txt.tmp
+        mv gdal_dict.txt.tmp gdal_dict.txt
     )
 fi
 
 EXCLUDED_FILES="*/.svn*,*/.git/*,configure,config.log,config.status,config.guess,config.sub,*/autom4te.cache/*,*.ai,*.svg"
+if [ -z ${AUTHORIZED_LIST+x} ]; then export AUTHORIZED_LIST=""; fi
 AUTHORIZED_LIST="$AUTHORIZED_LIST,te" # gdalwarp switch
 AUTHORIZED_LIST="$AUTHORIZED_LIST,LaTeX,BibTeX"
 AUTHORIZED_LIST="$AUTHORIZED_LIST,ALOS,Alos"
 AUTHORIZED_LIST="$AUTHORIZED_LIST,lon,Lon,LON"
 # New Mintpy ones
 AUTHORIZED_LIST="$AUTHORIZED_LIST,alos,ALOS,alosStack"
-AUTHORIZED_LIST="$AUTHORIZED_LIST,NED"
+AUTHORIZED_LIST="$AUTHORIZED_LIST,NED,LOD,Lod,lod"
 AUTHORIZED_LIST="$AUTHORIZED_LIST,waterMask,watermask"
 AUTHORIZED_LIST="$AUTHORIZED_LIST,smallbaselineApp"
 AUTHORIZED_LIST="$AUTHORIZED_LIST,Nealy" # Author in reference
 
-python fix_typos/codespell/codespell.py -w -i 3 -q 2 -S "$EXCLUDED_FILES,./autotest/*,./build*/*" \
+python fix_typos/codespell/codespell.py -w -i 3 -q 2 -S "$EXCLUDED_FILES,./autotest/*,./build*/*,./fix_typos/*" \
     --words-white-list="$AUTHORIZED_LIST" \
     -D ./fix_typos/gdal_dict.txt .

scripts/run_stripmap_stack.sh

@@ -2,7 +2,7 @@
 
 # clean folders before re-run
 if [ -d "Igrams" ]; then
-    echo "clean obsolete files/folders before reruning"
+    echo "clean obsolete files/folders before rerunning"
     rm -r baselines/ configs/ coregSLC/ geom_reference/ Igrams/ merged/ offsets/ refineSecondaryTiming/ run_files/ SLC/
     rm run_unPackALOS
     cd download

src/mintpy/cli/view.py

@@ -150,7 +150,7 @@ def cmd_line_parse(iargs=None):
             parser.error("--dem-blend requires -d/-dem.")
         # --cbar-ext option is ignored
         if '--cbar-ext' in inps.argv:
-            print('WARNING: --cbar-ext is NOT compatiable with --dem-blend, ignore --cbar-ext and continue.')
+            print('WARNING: --cbar-ext is NOT compatible with --dem-blend, ignore --cbar-ext and continue.')
 
     # check: conflicted options (geo-only options if inpput file is in radar-coordinates)
     geo_opt_names = ['--coord', '--show-gps', '--coastline', '--lalo-label', '--lalo-step', '--scalebar', '--faultline']

src/mintpy/data/colormaps/differences.cpt

@@ -1,5 +1,5 @@
 # GMT colour palette table (cpt)
-# grass2cpt ouput
+# grass2cpt output
 # COLOR_MODEL = RGB
 -1.000000e+00   0   0 255 0.000000e+00 255 255 255
 0.000000e+00 255 255 255 1.000000e+00 255   0   0

src/mintpy/plot_network.py

@@ -207,7 +207,8 @@ def plot_network(inps):
             print(f'save figure to {fig_names[2]}')
 
         # Fig 3 - Coherence Matrix
-        fig, ax = plt.subplots(figsize=[max(inps.fig_size), max(inps.fig_size)])
+        fig_size3 = np.mean(inps.fig_size)
+        fig, ax = plt.subplots(figsize=[fig_size3, fig_size3])
         ax = pp.plot_coherence_matrix(
             ax,
             inps.date12List,

src/mintpy/simulation/fractal.py

@@ -121,7 +121,7 @@ def fractal_surface_atmos(shape=(128, 128), resolution=60., p0=1., freq0=1e-3,
     # get the fractal spectrum and transform to spatial domain
     Hfrac = np.divide(H, fraction)
     fsurf = pyfftw.interfaces.numpy_fft.ifft2(Hfrac)
-    fsurf = np.abs(fsurf, dtype=np.float32)
+    fsurf = np.abs(fsurf).astype(np.float32)
     fsurf -= np.mean(fsurf)
 
     # calculate the power spectral density of 1st realization
@@ -130,7 +130,7 @@ def fractal_surface_atmos(shape=(128, 128), resolution=60., p0=1., freq0=1e-3,
     # scale the spectrum to match the input power spectral density.
     Hfrac *= np.sqrt(p0/p1)
     fsurf = pyfftw.interfaces.numpy_fft.ifft2(Hfrac)
-    fsurf = np.abs(fsurf, dtype=np.float32)
+    fsurf = np.abs(fsurf).astype(np.float32)
     fsurf -= np.mean(fsurf)
     return fsurf
 

src/mintpy/utils/plot.py

@@ -2217,7 +2217,7 @@ def prep_blend_image(data, dem, vmin=None, vmax=None, cmap='viridis',
         vert_exag=vert_exag,
     )
 
-    # add tranparency layer to the array (defualt: all ones = opaque)
+    # add tranparency layer to the array (default: all ones = opaque)
     illum_rgb = np.dstack([illum_rgb, np.ones_like(illum_rgb[:, :, 0])])
 
     ## masking the shaded-relief image:

src/mintpy/version.py

@@ -8,6 +8,7 @@
 ###########################################################################
 Tag = collections.namedtuple('Tag', 'version date')
 release_history = (
+    Tag('1.5.3', '2023-11-23'),
     Tag('1.5.2', '2023-08-09'),
     Tag('1.5.1', '2023-01-03'),
     Tag('1.5.0', '2022-11-18'),