add ee files

Serapieum-of-alex · Sep 21, 2022 · 5ddce9a · 5ddce9a
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diff --git a/.coveralls.yml b/.coveralls.yml
@@ -1,3 +1,2 @@
 repo_token: hxJrvjqiH2xBI7eit7BAb7FidH0LeYpGq
 service_name: github-action
-
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -48,11 +48,11 @@ jobs:
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
-        
+
         # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
         # queries: security-extended,security-and-quality
 
-        
+
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
@@ -61,7 +61,7 @@ jobs:
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 
-    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
     #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
 
     # - run: |

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -62,4 +62,4 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage1.xml,./coverage2.xml
-          directory: ./coverage/reports/
+          directory: ./coverage/reports/
diff --git a/.gitignore b/.gitignore
@@ -147,3 +147,6 @@ build_artifacts
 mo_*
 conda/
 /examples/data/ecmwf/daily/*
+.idea/*
+poetry.lock
+pyproject.toml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,12 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
-    hooks:
-#    -   id: check-yaml
-#        name: "[yaml -  check] validate yaml"
-    -   id: end-of-file-fixer
-        name: "[py -  check] validate yaml"
-    -   id: trailing-whitespace
-        name: "[file - format] trim trailing whitespace"
-        args: [ --markdown-linebreak-ext=md ]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.3.0
+  hooks:
+    - id: end-of-file-fixer
+      name: "[py -  check] validate yaml"
+    - id: trailing-whitespace
+      name: "[file - format] trim trailing whitespace"
+      args: [ --markdown-linebreak-ext=md ]
     -   id: check-added-large-files
         name: "[file -  check] large file"
         args: [ --maxkb=5000 ]
@@ -37,41 +35,51 @@ repos:
                 --no-sort-keys ]
     -   id: requirements-txt-fixer
         name: "[reqs - format] fix requirements.txt"
+    -   id: check-yaml
+        name: "[yaml -  check] validate yaml"
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.4
+  hooks:
+    - id: docformatter
+      name: "[py   - format] docformatter"
+      args: [ -i, --wrap-summaries, "0" ]
 
-#    - repo: https://github.com/PyCQA/docformatter
-#      rev: v1.4
-#      hooks:
-#        - id: docformatter
-##          name: "[py   - format] docformatter"
-##          args: [ -i, --wrap-summaries, "0" ]
+- repo: https://github.com/PyCQA/pydocstyle
+  rev: 6.1.1
+  hooks:
+    - id: pydocstyle
+      name: "[py   - check] pydocstyle"
+      files: ^Hapi/
 
-#    - repo: https://github.com/PyCQA/pydocstyle
-#      rev: 6.1.1
-#      hooks:
-#        - id: pydocstyle
-#          name: "[py   - check] pydocstyle"
-#          files: ^Hapi/
-    # TODO : uncheck later and fix all the problems of line too long
-#-   repo: https://gitlab.com/pycqa/flake8
-#    rev: 3.8.4
-#    hooks:
-#      - id: flake8
-#        name: "[py   - check] flake8"
-#        language_version: python3.8
-# TODO : this hook does not fix the files
-    #-   repo: https://github.com/psf/black
-#    rev: 19.3b0
-#    hooks:
-#    -   id: black
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.7.0
-    hooks:
-      - id: isort
-        name: "[py   - format] isort"
+- repo: https://gitlab.com/pycqa/flake8
+  rev: 3.8.4
+  hooks:
+    - id: flake8
+      name: "[py   - check] flake8"
+      language_version: python3.9
+      exclude: ^(examples/|tests/)
 
-#- repo: https://github.com/ambv/black
-#  rev: 20.8b1
-#  hooks:
-#    - id: black
-#      name: "[py   - format] black"
-#      language_version: python3.8
+- repo: https://github.com/psf/black
+  rev: 22.8.0
+  hooks:
+    - id: black
+- repo: https://github.com/pre-commit/mirrors-isort
+  rev: v5.7.0
+  hooks:
+    - id: isort
+      name: "[py   - format] isort"
+- repo: https://github.com/ambv/black
+  rev: 22.8.0
+  hooks:
+    - id: black
+      name: "[py   - format] black"
+      language_version: python3.9
+
+- repo: local
+  hooks:
+    - id: pytest-check
+      name: pytest-check
+      entry: pytest
+      language: system
+      pass_filenames: false
+      always_run: true
diff --git a/README.md b/README.md
@@ -25,12 +25,12 @@ earthobserve
 
 Main Features
 -------------
-  - 
+  -
 
 
 Future work
 -------------
-  - 
+  -
 
 
 

diff --git a/clone.json b/clone.json
@@ -1,4 +1,4 @@
 {
-  "message": "Must have push access to repository",
-  "documentation_url": "https://docs.github.com/rest/reference/repos#get-repository-clones"
+    "message": "Must have push access to repository",
+    "documentation_url": "https://docs.github.com/rest/reference/repos#get-repository-clones"
 }
diff --git a/docs/conf.py b/docs/conf.py
@@ -9,18 +9,17 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-# General information about the project.
-project = u"pyramids"
-author = "Mostafa Farrag"
-
-# copyright = u"2013-2019, "
-
-
 import os
 import sys
 
 # import sphinx_rtd_theme
 
+# General information about the project.
+project = "pyramids"
+author = "Mostafa Farrag"
+
+# copyright = u"2013-2019, "
+
 html_theme = "sphinxdoc"
 # html_theme = "agogo"
 html_theme_path = ["."]
@@ -207,7 +206,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ("index", "pyramids.tex", u"pyramids Documentation", u"Mostafa Farrag", "report")
+    ("index", "pyramids.tex", "pyramids Documentation", "Mostafa Farrag", "report")
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -250,8 +249,8 @@
     (
         "index",
         "pyramids",
-        u"pyramids Documentation",
-        u"Mostafa Farrag",
+        "pyramids Documentation",
+        "Mostafa Farrag",
         "pyramids",
         "One line description of project.",
         "Miscellaneous",

diff --git a/earth2observe/__init__.py b/earth2observe/__init__.py
@@ -13,7 +13,7 @@
 
 # documentation format
 __author__ = "Mostafa Farrag"
-__email__ = '[email protected]'
+__email__ = "[email protected]"
 __docformat__ = "restructuredtext"
 
 # Let users know if they're missing any of our hard dependencies
@@ -25,30 +25,32 @@
         __import__(dependency)
     except ImportError as e:
         missing_dependencies.append(dependency)
+        print(e)
 
 if missing_dependencies:
     raise ImportError("Missing required dependencies {0}".format(missing_dependencies))
 
-def configuration(parent_package='',top_path=None):
+
+def configuration(parent_package="", top_path=None):
 
     from numpy.distutils.misc_util import Configuration
 
-    config = Configuration(None,parent_package,top_path)
+    config = Configuration(None, parent_package, top_path)
     config.set_options(
         ignore_setup_xxx_py=True,
         assume_default_configuration=True,
         delegate_options_to_subpackages=True,
         quiet=True,
     )
 
-    config.add_subpackage('gee')
+    config.add_subpackage("gee")
     return config
 
 
-import earth2observe.chirps as chirps
-import earth2observe.ecmwf as ecmwf
-import earth2observe.gee as gee
-import earth2observe.utils as utils
+# import earth2observe.chirps as chirps
+# import earth2observe.ecmwf as ecmwf
+# import earth2observe.gee as gee
+# import earth2observe.utils as utils
 
 __doc__ = """
 earth2observe - remote sensing package

diff --git a/earth2observe/chirps.py b/earth2observe/chirps.py
@@ -1,27 +1,28 @@
-import os
 import datetime as dt
+import os
+from ftplib import FTP
+
 import numpy as np
 import pandas as pd
-from ftplib import FTP
 from joblib import Parallel, delayed
 from osgeo import gdal
 from pyramids.raster import Raster
-from earth2observe.utils import print_progress_bar, extractFromGZ
+
+from earth2observe.utils import extractFromGZ, print_progress_bar
 
 
 class CHIRPS:
-    """
-    CHIRPS
-    """
+    """CHIRPS."""
+
     def __init__(
-            self,
-            start: str="",
-            end: str="",
-            lat_lim: list=[],
-            lon_lim: list=[],
-            time: str="daily",
-            path: str="",
-            fmt: str="%Y-%m-%d",
+        self,
+        start: str = "",
+        end: str = "",
+        lat_lim: list = [],
+        lon_lim: list = [],
+        time: str = "daily",
+        path: str = "",
+        fmt: str = "%Y-%m-%d",
     ):
         """CHIRPS.
 
@@ -52,7 +53,9 @@ def __init__(
             self.output_folder = os.path.join(path, "Precipitation", "CHIRPS", "Daily")
         elif time == "monthly":
             self.time_freq = "MS"
-            self.output_folder = os.path.join(path, "Precipitation", "CHIRPS", "Monthly")
+            self.output_folder = os.path.join(
+                path, "Precipitation", "CHIRPS", "Monthly"
+            )
         else:
             raise KeyError("The input time interval is not supported")
         self.time = time
@@ -94,16 +97,17 @@ def __init__(
             self.lon_lim = lon_lim
         # Define IDs
         self.yID = 2000 - np.int16(
-            np.array([np.ceil((lat_lim[1] + 50) * 20), np.floor((lat_lim[0] + 50) * 20)])
+            np.array(
+                [np.ceil((lat_lim[1] + 50) * 20), np.floor((lat_lim[0] + 50) * 20)]
+            )
         )
         self.xID = np.int16(
             np.array(
                 [np.floor((lon_lim[0] + 180) * 20), np.ceil((lon_lim[1] + 180) * 20)]
             )
         )
 
-
-    def Download(self, progress_bar: bool=True, cores=None):
+    def Download(self, progress_bar: bool = True, cores=None):
         """Download.
 
         Download method downloads CHIRPS data
@@ -162,7 +166,6 @@ def Download(self, progress_bar: bool=True, cores=None):
             )
         return results
 
-
     @staticmethod
     def RetrieveData(Date, args):
         """RetrieveData.
@@ -198,8 +201,8 @@ def RetrieveData(Date, args):
         # Define FTP path to directory
         if TimeCase == "daily":
             pathFTP = (
-                    "pub/org/chg/products/CHIRPS-2.0/global_daily/tifs/p05/%s/"
-                    % Date.strftime("%Y")
+                "pub/org/chg/products/CHIRPS-2.0/global_daily/tifs/p05/%s/"
+                % Date.strftime("%Y")
             )
         elif TimeCase == "monthly":
             pathFTP = "pub/org/chg/products/CHIRPS-2.0/global_monthly/tifs/"
@@ -263,7 +266,7 @@ def RetrieveData(Date, args):
             dataset, NoDataValue = Raster.getRasterData(src)
 
             # clip dataset to the given extent
-            data = dataset[yID[0]: yID[1], xID[0]: xID[1]]
+            data = dataset[yID[0] : yID[1], xID[0] : xID[1]]
             # replace -ve values with -9999
             data[data < 0] = -9999
 
@@ -281,14 +284,13 @@ def RetrieveData(Date, args):
             os.remove(outfilename)
 
         except PermissionError:
-            print("The file covering the whole world could not be deleted please delete it after the download ends")
+            print(
+                "The file covering the whole world could not be deleted please delete it after the download ends"
+            )
         return True
 
-
     def ListAttributes(self):
-        """
-        Print Attributes List
-        """
+        """Print Attributes List."""
 
         print("\n")
         print(
@@ -300,4 +302,4 @@ def ListAttributes(self):
             if key != "name":
                 print(str(key) + " : " + repr(self.__dict__[key]))
 
-        print("\n")
+        print("\n")