setup pre-commit hook + initial run against all files (#852)

+ install pre-commit GitHub Apps

+ add `.pre-commit-config.yaml`

+ changes from the initial run of pre-commit against all files
   - end-of-file-fixer
   - trailing-whitespace
   - sort imports via isort
   - modernize python via pyupgrade

+ info: printout h5 dataset compression info

+ tests: consistent script header comments

+ utils.readfile: use MACRO_CASE global var - replace standardMetadataKeys with STD_METADATA_KEYS

Author: yunjunz

.github/ISSUE_TEMPLATE/feature_request.md

@@ -29,10 +29,9 @@ assignees: ''
 <!-- Add any other context about the feature request here. -->
 
 
-**Are you willing to help implement and maintain this feature?** 
+**Are you willing to help implement and maintain this feature?**
 
 - [ ] Yes
 - [ ] No
 
 <!-- Every feature we add is code that we will have to maintain and keep updated. This takes a lot of effort. If you are willing to be involved in the project and help maintain your feature, it will make it easier for us to accept it. -->
-

.github/config.yml

@@ -20,6 +20,6 @@ newPRWelcomeComment: >
 
 # Comment to be posted to on pull requests merged by a first time user
 firstPRMergeComment: >
-  🎉 🎉 🎉  Congrats on merging your first pull request! We here at behaviorbot are proud of you! 🎉 🎉 🎉 
+  🎉 🎉 🎉  Congrats on merging your first pull request! We here at behaviorbot are proud of you! 🎉 🎉 🎉
 
 # It is recommend to include as many gifs and emojis as possible

.github/workflows/publish-to-test-pypi.yml

@@ -55,4 +55,3 @@ jobs:
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}
         verbose: true
-

.gitignore

@@ -131,4 +131,4 @@ venv.bak/
 dmypy.json
 
 # Pyre type checker
-.pyre/
+.pyre/

.pre-commit-config.yaml

@@ -0,0 +1,77 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+ci:
+  autofix_prs: false
+
+fail_fast: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.3.0"
+    hooks:
+      - id: check-added-large-files
+        args: ['--maxkb=20']
+        exclude_types: [image]
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+        exclude: tests/data/
+
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.10.1"
+    hooks:
+      - id: isort
+        name: sort imports
+        args: ['--multi-line=VERTICAL_HANGING_INDENT',
+               '--trailing-comma',
+               '--combine-as']
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: "v2.37.3"
+    hooks:
+      - id: pyupgrade
+        name: modernize python
+        args: ['--py36-plus']
+
+
+  ############################################################
+  #- repo: https://github.com/psf/black
+  #  rev: "22.6.0"
+  #  hooks:
+  #    - id: black
+
+  #- repo: https://github.com/PyCQA/flake8
+  #  rev: "5.0.4"
+  #  hooks:
+  #    - id: flake8
+
+  #- repo: https://github.com/pre-commit/mirrors-mypy
+  #  rev: "v0.971"
+  #  hooks:
+  #    - id: mypy
+
+  #- repo: https://github.com/hadialqattan/pycln
+  #  rev: "v2.1.1"
+  #  hooks:
+  #    - id: pycln
+
+  #- repo: https://github.com/PyCQA/pydocstyle
+  #  rev: "6.1.1"
+  #  hooks:
+  #    - id: pydocstyle
+  #      additional_dependencies: [toml]
+  #      exclude: test
+
+  #- repo: https://github.com/sirosen/texthooks
+  #  rev: "0.3.1"
+  #  hooks:
+  #    - id: fix-ligatures
+  #    - id: fix-smartquotes

.readthedocs.yaml

@@ -22,4 +22,3 @@ python:
   version: 3.7
   install:
     - requirements: docs/requirements4rtd.txt
-

LICENSE

@@ -1,7 +1,7 @@
 Copyright (c) 2016, Zhang Yunjun and Heresh Fattahi
 Copyright (c) 2013, Heresh Fattahi
 
-This is free software; you can redistribute it and/or modify it 
+This is free software; you can redistribute it and/or modify it
 under the terms of the GNU General Public License as published by
 the Free Software Foundation; either version 3 of the License, or
 (at your option) any later version.

MANIFEST.in

@@ -3,4 +3,3 @@ include docs/README.md
 
 # Include the license file
 include LICENSE
-

docs/CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing Guidelines
 
-This document is inspired by similar instructions from numpy, GMT, ISCE, gdal and jupyterhub. If you're reading this section, you're probably interested in contributing to MintPy. Welcome and thanks for your interest in contributing! 
+This document is inspired by similar instructions from numpy, GMT, ISCE, gdal and jupyterhub. If you're reading this section, you're probably interested in contributing to MintPy. Welcome and thanks for your interest in contributing!
 
 These are several ways to contribute to the MintPy project:
 
@@ -14,7 +14,7 @@ These are several ways to contribute to the MintPy project:
 If you get stuck at any point you can open an [issue on GitHub](https://github.com/insarlab/MintPy/issues) or comment on any open issue or pull request or contact us on the [user forum](https://groups.google.com/forum/#!forum/mintpy).
 
 For more information on contributing to open source projects, [GitHub's own guide](https://guides.github.com/activities/contributing-to-open-source/)
-is a great starting point if you are new to version control. 
+is a great starting point if you are new to version control.
 
 ## Development process ##
 

docs/FAQs.md

@@ -8,7 +8,7 @@ For LOS displacement (velocity) in the unit of meters (m/yr), i.e. 'timeseries'
 
 ### 2. How to prepare the input for MintPy if I am using currently un-supported InSAR softwares?
 
-The input of MintPy routine workflow (`smallbaselineApp.py`) is a stack of unwrapped interferograms. For "stack", we mean all the interferograms (unwrapped phase and spatial coherence) and geometries (DEM, incidence angle, etc.) have the same spatial extent and same spatial resolution, either in geo-coordinates or radar (range-doppler) coordinates. The input has 2 components: data and attributes. 
+The input of MintPy routine workflow (`smallbaselineApp.py`) is a stack of unwrapped interferograms. For "stack", we mean all the interferograms (unwrapped phase and spatial coherence) and geometries (DEM, incidence angle, etc.) have the same spatial extent and same spatial resolution, either in geo-coordinates or radar (range-doppler) coordinates. The input has 2 components: data and attributes.
 
 All inputs are saved into the following HDF5 files during the data loading process in MintPy:
 
@@ -52,7 +52,7 @@ Note that MintPy assumes **date1_date2** convention for interferograms (date1 <
 
 #### Attributes
 
-For each data file, MintPy requires some attributes/metadata in `ROI_PAC .rsc` format as described [here](https://mintpy.readthedocs.io/en/latest/api/attributes/). The optional attributes are highly recommend. The interferogram specific attributes (DATE12, P_BASELINE_TOP/BOTTOM_HDR) is not needed for geometry files (DEM, incidence angle, etc.). 
+For each data file, MintPy requires some attributes/metadata in `ROI_PAC .rsc` format as described [here](https://mintpy.readthedocs.io/en/latest/api/attributes/). The optional attributes are highly recommend. The interferogram specific attributes (DATE12, P_BASELINE_TOP/BOTTOM_HDR) is not needed for geometry files (DEM, incidence angle, etc.).
 
 For the supported InSAR software workflows, we prepare these metadata via `prep_isce.py`, `prep_gamma.py`, etc., to read their native metadata, convert and write them into `ROI_PAC .rsc` style for each data file.