From 2f49382bc0f01cea89e57b1856b47a785f4255b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sat, 23 Nov 2024 22:43:28 +0100
Subject: [PATCH 01/13] Update workflow actions (#102)

* update workflow actions

* fix codecov token

* fix codecov token

* fix repository not found with slug

* use codecov action v4

* use codecov action v4

* update snyk action

* update snyk action

* fix snyk action

* setup snyk action for python

* setup snyk action for python

* setup snyk action for python

* setup snyk action for python

* setup snyk action for python
---
 .github/workflows/main.yml | 38 +++++++++++++++++++-------------------
 environment.yml            |  5 +----
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9b67109..5f36cdb 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -9,13 +9,13 @@ jobs:
         matrix:
             os: ["ubuntu-latest"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: snyk/actions/setup@master
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
           environment-file: environment.yml
-          python-version: 3.8
+          python-version: 3.9
+          use-mamba: true
           auto-activate-base: true
           
       - shell: bash -l {0}
@@ -29,7 +29,7 @@ jobs:
             pip install -e .
             
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           # Full git history is needed to get a proper list of changed files within `super-linter`
           fetch-depth: 0 
@@ -48,26 +48,26 @@ jobs:
         run: |
           pip install pytest
           pip install pytest-cov
-          pytest --cov=./ --cov-report=xml
+          pytest --cov --junitxml=junit.xml -o junit_family=legacy
         env:
           SH_CLIENT_ID: ${{ secrets.SH_CLIENT_ID }}
           SH_CLIENT_SECRET: ${{ secrets.SH_CLIENT_SECRET }}
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
         with:
-          directory: ./coverage/reports/
-          fail_ci_if_error: true
-          files: ./coverage.xml
-          flags: unittests
-          name: codecov-umbrella
-          path_to_write_report: ./coverage/codecov_report.txt
-          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
-      - name: Run Snyk to check for vulnerabilities
+      - name: Install dev requirements
+        shell: bash -l {0}
         run: |
           pip install -r dev-requirements.txt
-          snyk test --file=dev-requirements.txt --package-manager=pip --severity-threshold=high
+            
+      - name: Run Snyk to check for vulnerabilities
+        uses: snyk/actions/python@master
+        continue-on-error: true
         env:
-          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-          
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}          
+        with:
+          args: --file=dev-requirements.txt --package-manager=pip --severity-threshold=high --skip-unresolved=true
diff --git a/environment.yml b/environment.yml
index fce44eb..65dd7cd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,11 +1,8 @@
 name: earthspy
 channels:
-  - conda-forge/label/cf202003
-  - https://conda.software.inl.gov/public
-  - defaults
   - conda-forge
 dependencies:
-  - python=3
+  - python>=3.9
   - numpy
   - objectpath
   - pandas

From 4dd794893cf75001c8a4f9d222beb58031096f54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 24 Nov 2024 20:43:16 +0100
Subject: [PATCH 02/13] expand testing on python 3.10-3.12

* add macos and python versions

* remove python 3.9

* keep only ubuntu-latest for now
---
 .github/workflows/main.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5f36cdb..0cbb670 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -6,15 +6,16 @@ jobs:
     name: Setup and test
     runs-on: ${{ matrix.os }}
     strategy:
-        matrix:
-            os: ["ubuntu-latest"]
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.10", "3.11", "3.12"]
+        
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
           environment-file: environment.yml
-          python-version: 3.9
           use-mamba: true
           auto-activate-base: true
           

From f44ef666eec535903039c53984b7d09f5dc9202b Mon Sep 17 00:00:00 2001
From: Antsalacia <githubaddresstutanota@tutanota.com>
Date: Tue, 26 Nov 2024 15:04:27 +0100
Subject: [PATCH 03/13] Add metadata to tiff files (#103)

* add metadata to tiff files

* add the **kwargs in variable
---
 earthspy/earthspy.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/earthspy/earthspy.py b/earthspy/earthspy.py
index de6581d..0296aba 100644
--- a/earthspy/earthspy.py
+++ b/earthspy/earthspy.py
@@ -228,8 +228,13 @@ def get_available_data(self) -> list:
         # and update service_url if dowload failed
         try:
             # store metadata of available scenes
-            self.metadata = [list(iterator) for iterator in search_iterator]
-
+            self.metadata = {}
+            for iterator in search_iterator:
+                iterator_list = list(iterator)
+                if len(iterator_list) > 0:
+                    date = iterator_list[0]["properties"]["datetime"].split("T")[0]
+                    self.metadata[date] = iterator_list            
+                    
         except shb.exceptions.DownloadFailedException:
             # set specific base URL of deployment
             self.catalog_config.sh_base_url = shb.DataCollection[
@@ -250,8 +255,13 @@ def get_available_data(self) -> list:
             ]
 
             # store metadata of available scenes
-            self.metadata = [list(iterator) for iterator in search_iterator]
-
+            self.metadata = {}
+            for iterator in search_iterator:
+                iterator_list = list(iterator)
+                if len(iterator_list) > 0:
+                    date = iterator_list[0]["properties"]["datetime"].split("T")[0]
+                    self.metadata[date] = iterator_list  
+                    
         # create date +-1 hour around acquisition time
         time_difference = timedelta(hours=1)
 
@@ -1061,11 +1071,11 @@ def merge_rasters(self) -> None:
                         "transform": output_transform,
                     }
                 )
-
+                id_dict = {k:self.metadata[date][0][k] for k in ["id"]}
                 # write mosaic
                 with rasterio.open(date_output_filename, "w", **output_meta) as dst:
                     dst.write(mosaic)
-
+                    dst.update_tags(**id_dict)
                 # save file name of merged raster
                 self.output_filenames_renamed.append(date_output_filename)
 

From f2bfed8434f9cd44823b69cfe06dbbd265e1a895 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Tue, 26 Nov 2024 16:28:09 +0100
Subject: [PATCH 04/13] remove WIP badge (#105)

---
 README.org | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.org b/README.org
index c187917..06d0cd7 100644
--- a/README.org
+++ b/README.org
@@ -1,4 +1,3 @@
-[[https://www.repostatus.org/badges/latest/wip.svg][https://www.repostatus.org/badges/latest/wip.svg]]
 [[https://www.gnu.org/licenses/gpl-3.0][https://img.shields.io/badge/License-GPLv3-blue.svg]]
 [[https://github.com/AdrienWehrle/earthspy/actions][file:https://github.com/AdrienWehrle/earthspy/workflows/CI/badge.svg]]
 [[https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml][https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml/badge.svg]]

From 5ff5a9a370d3e6b85cf5751b2bd02cc52d07b2f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 1 Dec 2024 12:12:01 +0100
Subject: [PATCH 05/13] Enable pre-commit and add action (#108)

* enable pre-commit

* add pre-commit action

* fix test

* fix path

* remove line length in flake8

* set flake8 line length high enough

* set flake8 line length high enough
---
 .github/workflows/main.yml                    | 16 +--
 .github/workflows/pre-commit.yml              | 15 +++
 .gitignore                                    |  2 +-
 .pre-commit-config.yaml                       | 98 +++++++++++++++++++
 README.org                                    | 16 ++-
 docs/_build/html/_static/alabaster.css        |  2 +-
 docs/_build/html/_static/basic.css            |  2 +-
 .../html/_static/documentation_options.js     |  2 +-
 docs/_build/html/_static/language_data.js     |  2 -
 docs/_build/html/_static/pygments.css         |  2 +-
 docs/_build/html/_static/underscore.js        |  2 +-
 docs/_build/html/genindex.html                | 26 ++---
 docs/_build/html/index.html                   | 24 ++---
 docs/_build/html/search.html                  | 48 ++++-----
 docs/_build/html/searchindex.js               |  2 +-
 docs/api.rst                                  |  2 +-
 docs/generated/earthspy.rst                   | 19 ----
 docs/index.rst                                |  2 +-
 earthspy/__init__.py                          |  1 -
 earthspy/earthspy.py                          | 63 ++++++------
 earthspy/operational/earthspy_NRT.py          |  1 -
 setup.py                                      |  1 +
 tests/__init__.py                             |  1 -
 tests/test_earthspy.py                        | 20 ++--
 24 files changed, 234 insertions(+), 135 deletions(-)
 create mode 100644 .github/workflows/pre-commit.yml
 create mode 100644 .pre-commit-config.yaml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0cbb670..72237e3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -9,7 +9,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest"]
         python-version: ["3.10", "3.11", "3.12"]
-        
+
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -18,23 +18,23 @@ jobs:
           environment-file: environment.yml
           use-mamba: true
           auto-activate-base: true
-          
+
       - shell: bash -l {0}
         run: |
           conda info
           conda list
-          
+
       - name: Install earthspy
         shell: bash -l {0}
         run: |
             pip install -e .
-            
+
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           # Full git history is needed to get a proper list of changed files within `super-linter`
-          fetch-depth: 0 
-          
+          fetch-depth: 0
+
       - name: Lint code base
         uses: github/super-linter/slim@v4.9.0
         env:
@@ -64,11 +64,11 @@ jobs:
         shell: bash -l {0}
         run: |
           pip install -r dev-requirements.txt
-            
+
       - name: Run Snyk to check for vulnerabilities
         uses: snyk/actions/python@master
         continue-on-error: true
         env:
-          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}          
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         with:
           args: --file=dev-requirements.txt --package-manager=pip --severity-threshold=high --skip-unresolved=true
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
new file mode 100644
index 0000000..25ac772
--- /dev/null
+++ b/.github/workflows/pre-commit.yml
@@ -0,0 +1,15 @@
+name: Linting and formatting (pre-commit)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/action@v3.0.1
diff --git a/.gitignore b/.gitignore
index f294af6..cef40bf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -142,4 +142,4 @@ auth.txt
 *.gcno
 *.gcda
 *.gcov
-test_calculator
\ No newline at end of file
+test_calculator
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..aa9d759
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,98 @@
+# based on Glaciohack pre-commit config
+ci:
+    autofix_prs: false
+    autoupdate_schedule: quarterly
+repos:
+        - repo: https://github.com/pre-commit/pre-commit-hooks
+          rev: v5.0.0
+          hooks:
+                - id: check-yaml
+                - id: end-of-file-fixer
+                  exclude: \.txt$
+                - id: trailing-whitespace  # Remove trailing
+                                           # whitespaces
+                - id: check-merge-conflict
+        # Fix common spelling mistakes
+        - repo: https://github.com/codespell-project/codespell
+          rev: v2.3.0
+          hooks:
+                - id: codespell
+                  args: [
+                  '--ignore-words-list', 'alos,inout,vor',
+                    '--ignore-regex', '\bnin\b',
+                    '--'
+                  ]
+                  types_or: [python, rst, markdown]
+                  files: ^(earthspy|docs|tests)/
+
+        # Replace relative imports
+        - repo: https://github.com/MarcoGorelli/absolufy-imports
+          rev: v0.3.1
+          hooks:
+                - id: absolufy-imports
+
+        # Format the code aggressively using black
+        - repo: https://github.com/psf/black
+          rev: 24.10.0
+          hooks:
+                  - id: black
+                    args: [--line-length=88]
+
+        # Lint the code using flake8
+        - repo: https://github.com/pycqa/flake8
+          rev: 7.1.1
+          hooks:
+                - id: flake8
+                  args: [
+                          '--max-line-length', '122',
+                          '--extend-ignore', 'E203,B028', # flake8
+                                                          # disagrees
+                                                          # with
+                                                          # black, so
+                                                          # this
+                                                          # should be
+                                                          # ignored.
+                          '--'
+                  ]
+                  additional_dependencies:
+                          - flake8-comprehensions
+                          - flake8-bugbear
+                  files: ^(earthspy|tests)
+
+        # Sort imports using isort
+        - repo: https://github.com/PyCQA/isort
+          rev: 5.13.2
+          hooks:
+                  - id: isort
+                    args: [ "--profile", "black" ]
+
+        # Automatically upgrade syntax to a minimum version
+        - repo: https://github.com/asottile/pyupgrade
+          rev: v3.19.0
+          hooks:
+                - id: pyupgrade
+                  args: [--py37-plus]
+
+        # Various formattings
+        - repo: https://github.com/pre-commit/pygrep-hooks
+          rev: v1.10.0
+          hooks:
+                # Detect common mistake of using single backticks when
+                # writing rst
+                - id: rst-backticks
+                # Detect mistake of rst directive not ending with
+                # double colon or space before the double colon
+                - id: rst-directive-colons
+                  types: [text]
+                  types_or: [python, rst]
+                # Detect mistake of inline code touching normal text
+                # in rst
+                - id: rst-inline-touching-normal
+                  types: [text]
+                  types_or: [python, rst]
+                # Eval should never be used (can do arbitrary code
+                # execution)
+                - id: python-no-eval
+                # Enforce the use of type annotations instead of
+                # docstring type comments
+                - id: python-use-type-annotations
diff --git a/README.org b/README.org
index 06d0cd7..32a9000 100644
--- a/README.org
+++ b/README.org
@@ -8,13 +8,13 @@
 
 =earthspy= is a wrapper around methods for the download of satellite data offered in the [[https://github.com/sentinel-hub/sentinelhub-py][sentinelhub Python package]]. This tool makes the monitoring and study of any place on Earth simple, ready to use and easily deployable for operational purposes and automated Near-Real Time (NRT) applications.
 
-Some useful capabilities: 
+Some useful capabilities:
   - Data download in multiprocessing
-  - Data download at optimized resolutions with the Direct (D) download mode 
+  - Data download at optimized resolutions with the Direct (D) download mode
   - Data download at native resolutions with the Split and Merge (SM) downlodad mode
   - Data storage with efficient structure and file naming
 
-As =earthspy= is built on top of the [[https://www.sentinel-hub.com/][Sentinel Hub services]], it includes e.g. the data pre-processing through [[https://docs.sentinel-hub.com/api/latest/evalscript/][custom scripts]] allowing the user to process and download only the products needed (such as high-level indices) therefore optimizing download time and local storage. 
+As =earthspy= is built on top of the [[https://www.sentinel-hub.com/][Sentinel Hub services]], it includes e.g. the data pre-processing through [[https://docs.sentinel-hub.com/api/latest/evalscript/][custom scripts]] allowing the user to process and download only the products needed (such as high-level indices) therefore optimizing download time and local storage.
 
 * Table of Contents                               :toc_2:noexport:
 - [[#earthspy-%EF%B8%8F-earth_africa-earth_americas-earth_asia][earthspy]]
@@ -66,7 +66,12 @@ job = es.EarthSpy("/path/to/auth.txt")
 
 # as simple as it gets
 job.set_query_parameters(
-    bounding_box=[-51.13, 69.204, -51.06, 69.225], # format from doc: [min_x, min_y, max_x, max_y]
+    bounding_box=[
+        -51.13,
+        69.204,
+        -51.06,
+        69.225,
+    ],  # format from doc: [min_x, min_y, max_x, max_y]
     time_interval=["2019-08-03", "2019-08-10"],
     evaluation_script="https://custom-scripts.sentinel-hub.com/custom-scripts/sentinel-2/true_color/script.js",
     data_collection="SENTINEL2_L2A",
@@ -74,6 +79,7 @@ job.set_query_parameters(
 
 # and off it goes!
 job.send_sentinelhub_requests()
+
 #+end_src
 
 Homemade custom evalscripts can also be passed without effort to e.g. compute high-level indices (NDVI, NDSI...).
@@ -141,7 +147,7 @@ job.send_sentinelhub_requests()
 #+end_src
 
 
-* Operational Near Real-Time (NRT) deployment 
+* Operational Near Real-Time (NRT) deployment
 
 =earthspy= can be easily deployed for NRT monitoring. The setup is as simple as wrapping the query parameters in a short python script such as [[https://github.com/AdrienWehrle/earthspy/blob/main/earthspy/operational/earthspy_NRT.py][earthspy_NRT.py]] and including it in a cron job. See an example below where Sentinel-2 images of Ilulissat, Greenland acquired over the past three days are downloaded everyday at noon.
 #+BEGIN_SRC bash :results verbatim
diff --git a/docs/_build/html/_static/alabaster.css b/docs/_build/html/_static/alabaster.css
index 0eddaeb..969ce31 100644
--- a/docs/_build/html/_static/alabaster.css
+++ b/docs/_build/html/_static/alabaster.css
@@ -698,4 +698,4 @@ nav#breadcrumbs li+li:before {
     div.related {
         display: none;
     }
-}
\ No newline at end of file
+}
diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css
index bf18350..1c769a5 100644
--- a/docs/_build/html/_static/basic.css
+++ b/docs/_build/html/_static/basic.css
@@ -903,4 +903,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
\ No newline at end of file
+}
diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
index f1df40e..bef71d2 100644
--- a/docs/_build/html/_static/documentation_options.js
+++ b/docs/_build/html/_static/documentation_options.js
@@ -9,4 +9,4 @@ var DOCUMENTATION_OPTIONS = {
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false
-};
\ No newline at end of file
+};
diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js
index ebe2f03..7dbd658 100644
--- a/docs/_build/html/_static/language_data.js
+++ b/docs/_build/html/_static/language_data.js
@@ -293,5 +293,3 @@ function splitQuery(query) {
     }
     return result;
 }
-
-
diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css
index 87f8bd1..b35b845 100644
--- a/docs/_build/html/_static/pygments.css
+++ b/docs/_build/html/_static/pygments.css
@@ -79,4 +79,4 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .vg { color: #000000 } /* Name.Variable.Global */
 .highlight .vi { color: #000000 } /* Name.Variable.Instance */
 .highlight .vm { color: #000000 } /* Name.Variable.Magic */
-.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
\ No newline at end of file
+.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
diff --git a/docs/_build/html/_static/underscore.js b/docs/_build/html/_static/underscore.js
index cf177d4..542fe3c 100644
--- a/docs/_build/html/_static/underscore.js
+++ b/docs/_build/html/_static/underscore.js
@@ -3,4 +3,4 @@
 //     https://underscorejs.org
 //     (c) 2009-2021 Jeremy Ashkenas, Julian Gonggrijp, and DocumentCloud and Investigative Reporters & Editors
 //     Underscore may be freely distributed under the MIT license.
-var n="1.13.1",r="object"==typeof self&&self.self===self&&self||"object"==typeof global&&global.global===global&&global||Function("return this")()||{},t=Array.prototype,e=Object.prototype,u="undefined"!=typeof Symbol?Symbol.prototype:null,o=t.push,i=t.slice,a=e.toString,f=e.hasOwnProperty,c="undefined"!=typeof ArrayBuffer,l="undefined"!=typeof DataView,s=Array.isArray,p=Object.keys,v=Object.create,h=c&&ArrayBuffer.isView,y=isNaN,d=isFinite,g=!{toString:null}.propertyIsEnumerable("toString"),b=["valueOf","isPrototypeOf","toString","propertyIsEnumerable","hasOwnProperty","toLocaleString"],m=Math.pow(2,53)-1;function j(n,r){return r=null==r?n.length-1:+r,function(){for(var t=Math.max(arguments.length-r,0),e=Array(t),u=0;u<t;u++)e[u]=arguments[u+r];switch(r){case 0:return n.call(this,e);case 1:return n.call(this,arguments[0],e);case 2:return n.call(this,arguments[0],arguments[1],e)}var o=Array(r+1);for(u=0;u<r;u++)o[u]=arguments[u];return o[r]=e,n.apply(this,o)}}function _(n){var r=typeof 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-Search.setIndex({docnames:["api","generated/earthspy","index"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["api.rst","generated/earthspy.rst","index.rst"],objects:{"":[[1,0,0,"-","earthspy"]]},objnames:{"0":["py","module","Python module"]},objtypes:{"0":"py:module"},terms:{api:2,index:2,modul:2,page:2,search:2},titles:["API","earthspy","Welcome to earthspy\u2019s documentation!"],titleterms:{api:0,content:2,document:2,earthspi:[1,2],indic:2,s:2,tabl:2,welcom:2}})
\ No newline at end of file
+Search.setIndex({docnames:["api","generated/earthspy","index"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["api.rst","generated/earthspy.rst","index.rst"],objects:{"":[[1,0,0,"-","earthspy"]]},objnames:{"0":["py","module","Python module"]},objtypes:{"0":"py:module"},terms:{api:2,index:2,modul:2,page:2,search:2},titles:["API","earthspy","Welcome to earthspy\u2019s documentation!"],titleterms:{api:0,content:2,document:2,earthspi:[1,2],indic:2,s:2,tabl:2,welcom:2}})
diff --git a/docs/api.rst b/docs/api.rst
index ced4568..fa15c80 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -9,7 +9,7 @@ API
    :recursive:
 
    earthspy
-   
+
 
 .. automodule earthspy
 
diff --git a/docs/generated/earthspy.rst b/docs/generated/earthspy.rst
index 9e1db12..efebd77 100644
--- a/docs/generated/earthspy.rst
+++ b/docs/generated/earthspy.rst
@@ -2,22 +2,3 @@
 ========
 
 .. automodule:: earthspy
-
-   
-   
-   
-
-   
-   
-   
-
-   
-   
-   
-
-   
-   
-   
-
-
-
diff --git a/docs/index.rst b/docs/index.rst
index 4fbde63..8176788 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,7 +1,7 @@
 .. earthspy documentation master file, created by
    sphinx-quickstart on Mon May  2 20:38:22 2022.
    You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+   contain the root ``toctree`` directive.
 
 Welcome to earthspy's documentation!
 ====================================
diff --git a/earthspy/__init__.py b/earthspy/__init__.py
index 8b13789..e69de29 100644
--- a/earthspy/__init__.py
+++ b/earthspy/__init__.py
@@ -1 +0,0 @@
-
diff --git a/earthspy/earthspy.py b/earthspy/earthspy.py
index 0296aba..b0d9a22 100644
--- a/earthspy/earthspy.py
+++ b/earthspy/earthspy.py
@@ -1,45 +1,46 @@
-# -*- coding: utf-8 -*-
 """
 
 @author: Adrien Wehrlé, EO-IO, University of Zurich, Switzerland
 
 """
 
-from collections import Counter
-from datetime import datetime, timedelta
 import glob
 import json
+import os
+import shutil
+import tarfile
+import time
+from collections import Counter
+from datetime import datetime, timedelta
 from multiprocessing import cpu_count
+from pathlib import Path
+from typing import Tuple, Union
+
 import numpy as np
 import objectpath
-import os
 import pandas as pd
-from pathlib import Path
 import rasterio
-from rasterio.merge import merge
 import requests
 import sentinelhub as shb
-import shutil
-import tarfile
-import time
-from typing import Union, Tuple
 import validators
+from rasterio.merge import merge
 
 
 class EarthSpy:
-    """Monitor and study any place on Earth and in Near Real-Time (NRT) using the
-    SentinelHub services.
+    """Monitor and study any place on Earth and in Near Real-Time
+    (NRT) using the SentinelHub services.
+
     """
 
     def __init__(self, CLIENT_credentials_file: str) -> None:
         """
         :param CLIENT_credentials_file: full path to file containing credentials
-          with User's OAuth client ID (1st row) secrect (2nd row).
+          with User's OAuth client ID (1st row) secret (2nd row).
         :type CLIENT_credentials_file: str
         """
 
         # read credentials stored in text file
-        with open(CLIENT_credentials_file, "r") as file:
+        with open(CLIENT_credentials_file) as file:
             credentials = file.read().splitlines()
 
         # extract credentials from lines
@@ -49,8 +50,6 @@ def __init__(self, CLIENT_credentials_file: str) -> None:
         # setup connection
         self.configure_connection()
 
-        return None
-
     def configure_connection(self) -> shb.SHConfig:
         """Build a shb configuration class for the connection to Sentinel Hub services.
 
@@ -225,7 +224,7 @@ def get_available_data(self) -> list:
         ]
 
         # some data sets require a difference service_url, test search_iterator
-        # and update service_url if dowload failed
+        # and update service_url if download failed
         try:
             # store metadata of available scenes
             self.metadata = {}
@@ -233,8 +232,8 @@ def get_available_data(self) -> list:
                 iterator_list = list(iterator)
                 if len(iterator_list) > 0:
                     date = iterator_list[0]["properties"]["datetime"].split("T")[0]
-                    self.metadata[date] = iterator_list            
-                    
+                    self.metadata[date] = iterator_list
+
         except shb.exceptions.DownloadFailedException:
             # set specific base URL of deployment
             self.catalog_config.sh_base_url = shb.DataCollection[
@@ -260,8 +259,8 @@ def get_available_data(self) -> list:
                 iterator_list = list(iterator)
                 if len(iterator_list) > 0:
                     date = iterator_list[0]["properties"]["datetime"].split("T")[0]
-                    self.metadata[date] = iterator_list  
-                    
+                    self.metadata[date] = iterator_list
+
         # create date +-1 hour around acquisition time
         time_difference = timedelta(hours=1)
 
@@ -320,7 +319,7 @@ def get_raw_data_collection_resolution(self) -> int:
         return self.raw_data_collection_resolution
 
     def set_number_of_cores(self, nb_cores) -> int:
-        """Set number of cores if not specificed by user.
+        """Set number of cores if not specified by user.
 
         :return: Number of cores to use in multithreading.
         :rtype: int
@@ -353,7 +352,8 @@ def get_date_range(
         :rtype: pd.core.indexes.datetimes.DatetimeIndex
         """
 
-        # if an integer, create a datetimeIndex with the number of days from present date
+        # if an integer, create a datetimeIndex with the number of days
+        # from present date
         if isinstance(time_interval, int):
             # keep time_interval positive
             if time_interval < 0:
@@ -403,12 +403,12 @@ def get_bounding_box(self, bounding_box: Union[list, str]) -> shb.geometry.BBox:
         :rtype: sentinelhub.geometry.BBox
         """
 
-        # if a list, set Sentinel Hub BBox wit bounding_box
+        # if a list, set Sentinel Hub BBox with bounding_box
         if isinstance(bounding_box, list):
             # create Sentinel Hub BBox
             self.bounding_box = shb.BBox(bbox=bounding_box, crs=shb.CRS.WGS84)
 
-            # cant guess name, so set to None
+            # can't guess name, so set to None
             self.bounding_box_name = None
 
         # if a string, extract bounding box from corresponding GEOJSON file
@@ -472,7 +472,7 @@ def get_store_folder(self, store_folder: Union[str, None]) -> str:
             if self.algorithm:
                 store_folder += f"{os.sep}{self.algorithm}"
 
-        # create subfolder if doesnt exist
+        # create subfolder if doesn't exist
         if not os.path.exists(store_folder):
             os.makedirs(store_folder)
 
@@ -482,7 +482,7 @@ def get_store_folder(self, store_folder: Union[str, None]) -> str:
         return self.store_folder
 
     def convert_bounding_box_coordinates(self) -> Tuple[shb.geometry.BBox, list]:
-        """Convert bounding boxe coordinates to a Geodetic Parameter Dataset (EPSG) in
+        """Convert bounding box coordinates to a Geodetic Parameter Dataset (EPSG) in
         meter unit, default to EPSG:3413 (NSIDC Sea Ice Polar Stereographic
         North).
 
@@ -568,7 +568,7 @@ def set_correct_resolution(self) -> int:
         elif not self.resolution and self.download_mode == "SM":
             self.resolution = self.raw_data_collection_resolution
 
-        # resolution cant be higher than max resolution in D download mode
+        # resolution can't be higher than max resolution in D download mode
         if self.download_mode == "D" and self.resolution < max_resolution:
             self.resolution = max_resolution
             if self.verbose:
@@ -618,7 +618,8 @@ def get_optimal_box_split(self) -> Tuple[int, int]:
         boxes_pixels_x = (dx / trial_split_boxes) / self.resolution
         boxes_pixels_y = (dy / trial_split_boxes) / self.resolution
 
-        # get minimum number of split boxes needed to stay below Sentinel Hub max dimensions
+        # get minimum number of split boxes needed to stay below Sentinel Hub
+        # max dimensions
         min_nb_boxes_x = int(trial_split_boxes[np.where(boxes_pixels_x <= 2500)[0][0]])
         min_nb_boxes_y = int(trial_split_boxes[np.where(boxes_pixels_y <= 2500)[0][0]])
 
@@ -681,7 +682,7 @@ def set_split_boxes_ids(self) -> dict:
         """
 
         # store split boxes ids in dict
-        self.split_boxes_ids = {i: sb for i, sb in enumerate(self.split_boxes)}
+        self.split_boxes_ids = dict(zip(range(len(self.split_boxes)), self.split_boxes))
 
         return self.split_boxes_ids
 
@@ -1071,7 +1072,7 @@ def merge_rasters(self) -> None:
                         "transform": output_transform,
                     }
                 )
-                id_dict = {k:self.metadata[date][0][k] for k in ["id"]}
+                id_dict = {k: self.metadata[date][0][k] for k in ["id"]}
                 # write mosaic
                 with rasterio.open(date_output_filename, "w", **output_meta) as dst:
                     dst.write(mosaic)
diff --git a/earthspy/operational/earthspy_NRT.py b/earthspy/operational/earthspy_NRT.py
index d24644e..ab859df 100644
--- a/earthspy/operational/earthspy_NRT.py
+++ b/earthspy/operational/earthspy_NRT.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 """
 
 @author: Adrien Wehrlé, EO-IO, University of Zurich, Switzerland
diff --git a/setup.py b/setup.py
index 8bf1ba9..6068493 100644
--- a/setup.py
+++ b/setup.py
@@ -1,2 +1,3 @@
 from setuptools import setup
+
 setup()
diff --git a/tests/__init__.py b/tests/__init__.py
index 8b13789..e69de29 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -1 +0,0 @@
-
diff --git a/tests/test_earthspy.py b/tests/test_earthspy.py
index ffe06c7..f0d3da6 100644
--- a/tests/test_earthspy.py
+++ b/tests/test_earthspy.py
@@ -1,18 +1,19 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 """
 
 @author: Adrien Wehrlé, EO-IO, University of Zurich, Switzerland
 
 """
 
-import earthspy.earthspy as es
-import numpy as np
 import os
+
+import numpy as np
 import pandas as pd
 import requests
 import sentinelhub as shb
 
+import earthspy.earthspy as es
+
 
 class TestEarthspy:
     # create local variables from environment secrets for convenience
@@ -36,7 +37,8 @@ class TestEarthspy:
           // Set gain for visualisation
           let gain = 2.5;
           // Return RGB
-          return [sample.B04 * gain, sample.B03 * gain, sample.B02 * gain, sample.dataMask];
+          return [sample.B04 * gain, sample.B03 * gain, sample.B02 * gain,
+                  sample.dataMask];
         }
         """
 
@@ -100,7 +102,7 @@ def test_init(self) -> None:
         assert self.t1.config.sh_client_secret == os.environ["SH_CLIENT_SECRET"]
 
     def test_set_query_parameters(self) -> None:
-        """Test direct attribute assignement."""
+        """Test direct attribute assignment."""
 
         # check if attributes were set accordingly
         assert self.t1.download_mode is not None
@@ -249,9 +251,9 @@ def test_set_correct_resolution(self) -> None:
 
         r2 = self.t3.set_correct_resolution()
         # check that query resolution was set correctly
-        assert r1 == 10
+        assert r2 == 11
         # check that download mode was set correctly
-        assert isinstance(self.t1.download_mode, str)
+        assert isinstance(self.t3.download_mode, str)
 
     def test_list_requests(self) -> None:
         """Test request listing"""
@@ -299,9 +301,9 @@ def test_set_split_boxes_ids(self) -> None:
         """Test split box ID generation"""
 
         sbi1 = self.t1.set_split_boxes_ids()
-        # check that split box ids were saved in dictionnary
+        # check that split box ids were saved in dictionary
         assert isinstance(sbi1, dict)
-        # check that dictionnary has the right shape
+        # check that dictionary has the right shape
         assert len(sbi1) == 4
 
     def test_get_evaluation_script(self) -> None:

From 68437b46abc1f01e3189c66d6ac46a45d2744546 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 1 Dec 2024 14:40:48 +0100
Subject: [PATCH 06/13] Add CONTRIBUTING (#109)

* add isort badge

* bix isort badge

* bix isort badge

* bix isort badge

* refix badge

* add hyperlink to badge

* add hyperlink to badge

* add hyperlink to badge

* skeleton of CONTRIBUTING

* fix emojis

* fix precommit

* add precommit badge

* fix workflow

* add pre-commit hook to convert yml

* fix install of dev requirements

* fix contributing headers
---
 .../scripts/generate_pip_deps_from_conda.py   | 152 ++++++++++++++++++
 .github/workflows/main.yml                    |   4 +-
 .pre-commit-config.yaml                       |  14 ++
 CONTRIBUTING.org                              | 131 +++++++++++++++
 README.org                                    |   3 +
 dev-environment.yml                           |  22 +++
 dev-requirements.txt => requirements-dev.txt  |  10 +-
 7 files changed, 331 insertions(+), 5 deletions(-)
 create mode 100755 .github/scripts/generate_pip_deps_from_conda.py
 create mode 100644 CONTRIBUTING.org
 create mode 100644 dev-environment.yml
 rename dev-requirements.txt => requirements-dev.txt (50%)

diff --git a/.github/scripts/generate_pip_deps_from_conda.py b/.github/scripts/generate_pip_deps_from_conda.py
new file mode 100755
index 0000000..ac74bd5
--- /dev/null
+++ b/.github/scripts/generate_pip_deps_from_conda.py
@@ -0,0 +1,152 @@
+#!/usr/bin/env python3
+"""
+(Copied from pandas:
+https://github.com/pandas-dev/pandas/blob/main/scripts/generate_pip_deps_from_conda.py)
+Convert the conda environment.yml to the pip requirements-dev.txt, or
+check that they have the same packages (for the CI)
+
+Usage:
+
+    Generate `requirements-dev.txt`
+    $ python scripts/generate_pip_deps_from_conda.py
+
+    Compare and fail (exit status != 0) if `requirements-dev.txt` has not been
+    generated with this script:
+    $ python scripts/generate_pip_deps_from_conda.py --compare
+
+"""
+import argparse
+import pathlib
+import re
+import sys
+
+if sys.version_info >= (3, 11):
+    import tomllib
+else:
+    import tomli as tomllib
+import yaml
+
+EXCLUDE = {"python"}
+REMAP_VERSION = {"tzdata": "2022.1"}
+RENAME = {}
+
+
+def conda_package_to_pip(package: str):
+    """
+    Convert a conda package to its pip equivalent.
+
+    In most cases they are the same, those are the exceptions:
+    - Packages that should be excluded (in `EXCLUDE`)
+    - Packages that should be renamed (in `RENAME`)
+    - A package requiring a specific version, in conda is defined with a single
+      equal (e.g. ``pandas=1.0``) and in pip with two (e.g. ``pandas==1.0``)
+    """
+    package = re.sub("(?<=[^<>])=", "==", package).strip()
+    print(package)
+
+    for compare in ("<=", ">=", "=="):
+        if compare in package:
+            pkg, version = package.split(compare)
+            if pkg in EXCLUDE:
+                return
+            if pkg in REMAP_VERSION:
+                return "".join((pkg, compare, REMAP_VERSION[pkg]))
+            if pkg in RENAME:
+                return "".join((RENAME[pkg], compare, version))
+
+    if package in EXCLUDE:
+        return
+
+    if package in RENAME:
+        return RENAME[package]
+
+    return package
+
+
+def generate_pip_from_conda(
+    conda_path: pathlib.Path, pip_path: pathlib.Path, compare: bool = False
+) -> bool:
+    """
+    Generate the pip dependencies file from the conda file, or compare that
+    they are synchronized (``compare=True``).
+
+    Parameters
+    ----------
+    conda_path : pathlib.Path
+        Path to the conda file with dependencies (e.g. `environment.yml`).
+    pip_path : pathlib.Path
+        Path to the pip file with dependencies (e.g. `requirements-dev.txt`).
+    compare : bool, default False
+        Whether to generate the pip file (``False``) or to compare if the
+        pip file has been generated with this script and the last version
+        of the conda file (``True``).
+
+    Returns
+    -------
+    bool
+        True if the comparison fails, False otherwise
+    """
+    with conda_path.open() as file:
+        deps = yaml.safe_load(file)["dependencies"]
+
+    pip_deps = []
+    for dep in deps:
+        if isinstance(dep, str):
+            conda_dep = conda_package_to_pip(dep)
+            if conda_dep:
+                pip_deps.append(conda_dep)
+        elif isinstance(dep, dict) and len(dep) == 1 and "pip" in dep:
+            pip_deps.extend(dep["pip"])
+        else:
+            raise ValueError(f"Unexpected dependency {dep}")
+
+    header = (
+        f"# This file is auto-generated from {conda_path.name}, do not modify.\n"
+        "# See that file for comments about the need/usage of each dependency.\n\n"
+    )
+    pip_content = header + "\n".join(pip_deps) + "\n"
+
+    # Add setuptools to requirements-dev.txt
+
+    # with open(pathlib.Path(conda_path.parent, "pyproject.toml"), "rb") as fd:
+    #     meta = tomllib.load(fd)
+    # for requirement in meta["build-system"]["requires"]:
+    #     if "setuptools" in requirement:
+    #         pip_content += requirement
+    #         pip_content += "\n"
+
+    if compare:
+        with pip_path.open() as file:
+            return pip_content != file.read()
+
+    with pip_path.open("w") as file:
+        file.write(pip_content)
+    return False
+
+
+if __name__ == "__main__":
+    argparser = argparse.ArgumentParser(
+        description="convert (or compare) conda file to pip"
+    )
+    argparser.add_argument(
+        "--compare",
+        action="store_true",
+        help="compare whether the two files are equivalent",
+    )
+    args = argparser.parse_args()
+
+    conda_fname = "dev-environment.yml"
+    pip_fname = "requirements-dev.txt"
+    repo_path = pathlib.Path(__file__).parent.parent.parent.absolute()
+    res = generate_pip_from_conda(
+        pathlib.Path(repo_path, conda_fname),
+        pathlib.Path(repo_path, pip_fname),
+        compare=args.compare,
+    )
+    if res:
+        msg = (
+            f"`{pip_fname}` has to be generated with `{__file__}` after "
+            f"`{conda_fname}` is modified.\n"
+        )
+        sys.stderr.write(msg)
+    sys.exit(res)
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 72237e3..729f4bf 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -63,7 +63,7 @@ jobs:
       - name: Install dev requirements
         shell: bash -l {0}
         run: |
-          pip install -r dev-requirements.txt
+          pip install -r requirements-dev.txt
 
       - name: Run Snyk to check for vulnerabilities
         uses: snyk/actions/python@master
@@ -71,4 +71,4 @@ jobs:
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         with:
-          args: --file=dev-requirements.txt --package-manager=pip --severity-threshold=high --skip-unresolved=true
+          args: --file=requirements-dev.txt --package-manager=pip --severity-threshold=high --skip-unresolved=true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index aa9d759..4848f16 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -96,3 +96,17 @@ repos:
                 # Enforce the use of type annotations instead of
                 # docstring type comments
                 - id: python-use-type-annotations
+
+
+        - repo: local
+          hooks:
+            # Generate pip's dev-requirements.txt from conda's
+            # dev-environment.yml to run snyk (snyk doesn't currently
+            # support conda)
+            - id: pip-to-conda
+              name: Generate pip dependency from conda
+              language: python
+              entry: .github/scripts/generate_pip_deps_from_conda.py
+              files: ^(dev-environment.yml|requirements-dev.txt)$
+              pass_filenames: false
+              additional_dependencies: [tomli, pyyaml]
diff --git a/CONTRIBUTING.org b/CONTRIBUTING.org
new file mode 100644
index 0000000..d2cde9f
--- /dev/null
+++ b/CONTRIBUTING.org
@@ -0,0 +1,131 @@
+* Introduction
+
+First off, thank you for considering contributing to =earthspy=! 😊
+
+Following the guidelines presented here helps to communicate that you
+respect the efforts the developers managing and developing this open
+source project have put to foster community development. In return,
+they should reciprocate that respect in addressing your issue,
+assessing changes, and helping you finalize your pull requests. 🌻
+
+Any kind of contribution is more than welcome. Improving
+documentation, bug triaging, implementing new features or writing
+tutorials are all examples of helpful contributions. 🚀
+
+* Making a contribution
+
+** Overview
+
+ 1. Fork =AdrienWehrle/earthspy= and clone your fork repository locally.
+ 2. Set up the development environment (section below).
+ 3. Create a branch for the new feature or bug fix.
+ 4. Make your changes, and add or modify related tests in =tests/=.
+ 5. Commit, making sure to run pre-commit separately if not installed as git hook.
+ 6. Push to your fork.
+ 7. Open a pull request from GitHub to discuss and eventually merge.
+
+
+** Step by step
+
+*** Setup
+
+Clone the git repository and create a [[https://docs.conda.io/projects/conda/en/latest/index.html][conda]] or [[https://mamba.readthedocs.io/en/latest/index.html][mamba]] environment. If
+you use mamba (mamba is great), just replace =conda= for =mamba=
+below. Steps below are similar to those presented in the [[https://github.com/AdrienWehrle/earthspy/tree/main][README]] except
+=dev-environment.yml= is used here instead of =environment.yml= as it
+contains necessary dependencies for continuous integration and
+continuous development.
+
+#+begin_src shell :results verbatim
+
+# clone repository
+git clone git@github.com:AdrienWehrle/earthspy.git
+
+# move into earthspy directory
+cd earthspy
+
+# create conda environment
+conda env create -f dev-environment.yml
+
+# activate conda environment
+conda activate earthspy-dev
+
+# install earthspy
+pip install -e .
+
+#+end_src
+
+*** Tests
+
+If your PR targets the implementation of a new feature or the
+improvement of existing ones, please add at least one test per feature
+(in the associated =tests/test_earthspy.py= file) and include them in
+your PR, using =pytests= (see existing tests for examples).
+
+To run the entire test suite, run pytest in the current directory:
+
+#+begin_src shell :results verbatim
+pytest
+#+end_src
+
+
+*** Formatting and linting
+
+Before you make your commit, please install =pre-commit= (see
+[[https://pre-commit.com/][pre-commit documentation]]), which will use =.pre-commit-config.yaml= to
+verify spelling errors, import sorting, type checking, formatting and
+linting.
+
+You can then run =pre-commit= manually:
+
+#+begin_src shell :results verbatim
+pre-commit run --all-files
+#+end_src
+
+In your PR, make sure to note if all =pre-commit= checks passed or
+not. Other developers will gladly help you getting rid of remaining
+red signs in your terminal if you feel stuck! 🌿
+
+Optionally, =pre-commit= can also be installed as a git hook to
+automatically ensure checks have to pass before committing.
+
+Once all =pre-commit= checks have passed (or you need help),
+please commit your changes with short and clear messages.
+
+
+* Reporting a bug
+
+** Security disclosures
+
+If you find a security vulnerability, please do not open an
+issue. Email adrien.wehrle@hotmail.fr instead.
+
+In order to determine whether you are dealing with a security issue,
+ask yourself these two questions:
+
+- Can I access something that's not mine, or something I shouldn't
+  have access to?
+- Can I disable something for other people?
+
+** How to file a bug report
+
+When filing an issue at
+[[earthspy/issues][https://github.com/AdrienWehrle/earthspy/issues]], make sure to answer
+these five questions:
+
+- Have you installed =earthspy= using =environment.yml=? If not, what
+  version of Python and dependencies are you using?
+- What operating system and processor architecture are you using?
+- What did you do?
+- What did you expect to see?
+- What did you see instead?
+
+
+* Rights
+
+The license (see =LICENSE=) applies to all contributions.
+
+* Credits
+
+Part of this document is based on [[https://github.com/nayafia][nayafia]]'s [[https://github.com/nayafia/contributing-template/blob/master/CONTRIBUTING-template.md][CONTRIBUTING]] template and
+[[https://github.com/GlacioHack/geoutils/blob/main/CONTRIBUTING.md][geoutils CONTRIBUTING]].
diff --git a/README.org b/README.org
index 32a9000..9fff53a 100644
--- a/README.org
+++ b/README.org
@@ -1,8 +1,11 @@
 [[https://www.gnu.org/licenses/gpl-3.0][https://img.shields.io/badge/License-GPLv3-blue.svg]]
 [[https://github.com/AdrienWehrle/earthspy/actions][file:https://github.com/AdrienWehrle/earthspy/workflows/CI/badge.svg]]
 [[https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml][https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml/badge.svg]]
+[[https://pre-commit.com/][https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit.svg]]
 [[https://codecov.io/gh/AdrienWehrle/earthspy][https://codecov.io/gh/AdrienWehrle/earthspy/branch/main/graph/badge.svg]]
 [[https://github.com/psf/black][https://img.shields.io/badge/code%20style-black-000000.svg]]
+[[https://pycqa.github.io/isort/][https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336.svg]]
+
 
 * earthspy 🛰️ :earth_africa: :earth_americas: :earth_asia: :moon:
 
diff --git a/dev-environment.yml b/dev-environment.yml
new file mode 100644
index 0000000..52e488e
--- /dev/null
+++ b/dev-environment.yml
@@ -0,0 +1,22 @@
+name: earthspy-dev
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.9
+  - numpy
+  - objectpath
+  - pandas
+  - rasterio
+  - validators
+  - sentinelhub >= 3.4
+  - pip
+  - flake8
+  - pytest
+  - pytest-lazy-fixture
+  - sphinx
+  - sphinx_rtd_theme
+  - pylint
+  - sphinxcontrib_programoutput
+  - sphinx_autodoc_typehints
+  - pre-commit
+  - sphinx-gallery
diff --git a/dev-requirements.txt b/requirements-dev.txt
similarity index 50%
rename from dev-requirements.txt
rename to requirements-dev.txt
index 8d3ac43..23edc01 100644
--- a/dev-requirements.txt
+++ b/requirements-dev.txt
@@ -1,8 +1,13 @@
+# This file is auto-generated from dev-environment.yml, do not modify.
+# See that file for comments about the need/usage of each dependency.
+
 numpy
+objectpath
 pandas
-validators
 rasterio
-sentinelhub
+validators
+sentinelhub >= 3.4
+pip
 flake8
 pytest
 pytest-lazy-fixture
@@ -13,4 +18,3 @@ sphinxcontrib_programoutput
 sphinx_autodoc_typehints
 pre-commit
 sphinx-gallery
-

From 9e3e1887cdc8bb8a6cc382481f5786e0ce85927f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 1 Dec 2024 14:47:46 +0100
Subject: [PATCH 07/13] Add dependabot (#110)

---
 .github/dependabot.yml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100755 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100755
index 0000000..ac27a84
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,8 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

From 649bfef69c02d71a3df0cbca215bab51e3263c9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 1 Dec 2024 15:56:21 +0100
Subject: [PATCH 08/13] Fix doc requirements (#114)

* fix docs

* fix dependencies in dev-environment.yml

* fix environment

* fix environment

* switch back to pip for doc

* switch back to pip for doc

* fix requirements
---
 .readthedocs.yml     | 12 +++++++++---
 dev-environment.yml  |  6 ++++--
 environment.yml      |  1 +
 requirements-dev.txt |  4 ++--
 4 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index f0b29af..fb19340 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,17 +5,23 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: []
+formats: [pdf]
 
 python:
-  version: 3.7
   install:
-    - requirements: dev-requirements.txt
+    - requirements: requirements-dev.txt
     - method: pip
       path: .
diff --git a/dev-environment.yml b/dev-environment.yml
index 52e488e..18c217f 100644
--- a/dev-environment.yml
+++ b/dev-environment.yml
@@ -1,6 +1,8 @@
 name: earthspy-dev
 channels:
+  - defaults
   - conda-forge
+  - bioconda
 dependencies:
   - python>=3.9
   - numpy
@@ -16,7 +18,7 @@ dependencies:
   - sphinx
   - sphinx_rtd_theme
   - pylint
-  - sphinxcontrib_programoutput
-  - sphinx_autodoc_typehints
+  - sphinxcontrib-programoutput
+  - sphinx-autodoc-typehints
   - pre-commit
   - sphinx-gallery
diff --git a/environment.yml b/environment.yml
index 65dd7cd..56402e9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,5 +1,6 @@
 name: earthspy
 channels:
+  - defaults
   - conda-forge
 dependencies:
   - python>=3.9
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 23edc01..2d62fed 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -14,7 +14,7 @@ pytest-lazy-fixture
 sphinx
 sphinx_rtd_theme
 pylint
-sphinxcontrib_programoutput
-sphinx_autodoc_typehints
+sphinxcontrib-programoutput
+sphinx-autodoc-typehints
 pre-commit
 sphinx-gallery

From 13f786c39d1c43706f64f16f9ef1a1d22c840447 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Dec 2024 16:14:56 +0100
Subject: [PATCH 09/13] Bump github/super-linter from 4.9.0 to 5.0.0 (#113)

Bumps [github/super-linter](https://github.com/github/super-linter) from 4.9.0 to 5.0.0.
- [Release notes](https://github.com/github/super-linter/releases)
- [Changelog](https://github.com/github/super-linter/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/super-linter/compare/v4.9.0...v5.0.0)

---
updated-dependencies:
- dependency-name: github/super-linter
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 729f4bf..bf53d1b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,7 +36,7 @@ jobs:
           fetch-depth: 0
 
       - name: Lint code base
-        uses: github/super-linter/slim@v4.9.0
+        uses: github/super-linter/slim@v5.0.0
         env:
           VALIDATE_ALL_CODEBASE: true
           VALIDATE_JSON: true

From c6adb35721e3df683d30f438b2add8eefde96f43 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Dec 2024 16:15:10 +0100
Subject: [PATCH 10/13] Bump actions/checkout from 3 to 4 (#112)

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/codeql.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 2da8421..32fbd0f 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2

From e6b9a14763b71880a00879c301f617109b0e09d4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Dec 2024 16:15:23 +0100
Subject: [PATCH 11/13] Bump github/codeql-action from 2 to 3 (#111)

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/codeql.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 32fbd0f..483a9d9 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -27,15 +27,15 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

From d01f7d5038b576ded107e5e3ff7b05ff9f67628d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?= <adrien.wehrle@hotmail.fr>
Date: Sun, 1 Dec 2024 23:26:17 +0100
Subject: [PATCH 12/13] Translate README and CONTRIBUTING to markdown (#116)

* converting README org to md

* fixing missing translation

* fixing badges

* fixing badges

* fix table of content

* add contributing

* translate CONTRIBUTING

* fix table of contents
---
 CONTRIBUTING.md  | 140 +++++++++++++++++++++++++++++++++++++++
 CONTRIBUTING.org | 131 -------------------------------------
 README.md        | 167 +++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 307 insertions(+), 131 deletions(-)
 create mode 100644 CONTRIBUTING.md
 delete mode 100644 CONTRIBUTING.org
 create mode 100644 README.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..21e22a4
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,140 @@
+# Introduction
+
+First off, thank you for considering contributing to `earthspy`! 😊
+
+Following the guidelines presented here helps to communicate that you
+respect the efforts the developers managing and developing this open
+source project have put to foster community development. In return,
+they should reciprocate that respect in addressing your issue,
+assessing changes, and helping you finalize your pull requests. 🌻
+
+Any kind of contribution is more than welcome. Improving
+documentation, bug triaging, implementing new features or writing
+tutorials are all examples of helpful contributions. 🚀
+
+# Making a contribution
+
+## Overview
+
+ 1. Fork `AdrienWehrle/earthspy` and clone your fork repository locally.
+ 2. Set up the development environment (section below).
+ 3. Create a branch for the new feature or bug fix.
+ 4. Make your changes, and add or modify related tests in
+    [`tests/`](https://github.com/AdrienWehrle/earthspy/tree/main/tests).
+ 5. Commit, making sure to run pre-commit separately if not installed as git hook.
+ 6. Push to your fork.
+ 7. Open a pull request from GitHub to discuss and eventually merge.
+
+
+## Step by step
+
+### Setup
+
+Clone the git repository and create a
+[conda](https://docs.conda.io/projects/conda/en/latest/index.html) or
+[mamba](https://mamba.readthedocs.io/en/latest/index.html)
+environment. If you use mamba (mamba is great), just replace `conda`
+for `mamba` below. Steps below are similar to those presented in the
+[README](https://github.com/AdrienWehrle/earthspy/tree/main) except
+[`dev-environment.yml`](https://github.com/AdrienWehrle/earthspy/blob/main/dev-environment.yml)
+is used here instead of
+[`environment.yml`](https://github.com/AdrienWehrle/earthspy/blob/main/dev-environment.yml)
+as it contains necessary dependencies for continuous integration and
+continuous development.
+
+```bash
+
+# clone repository
+git clone git@github.com:AdrienWehrle/earthspy.git
+
+# move into earthspy directory
+cd earthspy
+
+# create conda environment
+conda env create -f dev-environment.yml
+
+# activate conda environment
+conda activate earthspy-dev
+
+# install earthspy
+pip install -e .
+```
+
+### Tests
+
+If your PR targets the implementation of a new feature or the
+improvement of existing ones, please add at least one test per feature
+(in the associated
+[`tests/test_earthspy.py`](https://github.com/AdrienWehrle/earthspy/blob/main/LICENSE)
+file) and include them in your PR, using `pytest` (see existing tests
+for examples).
+
+To run the entire test suite, run pytest in the current directory:
+
+```bash
+pytest
+```
+
+
+### Formatting and linting
+
+Before you make your commit, please install `pre-commit` (see
+[pre-commit documentation](https://pre-commit.com/)), which will use
+`.pre-commit-config.yaml` to verify spelling errors, import sorting,
+type checking, formatting and linting.
+
+You can then run `pre-commit` manually:
+
+```bash
+pre-commit run --all-files
+```
+
+In your PR, make sure to note if all `pre-commit` checks passed or
+not. Other developers will gladly help you getting rid of remaining
+red signs in your terminal if you feel stuck! 🌿
+
+Optionally, `pre-commit` can also be installed as a git hook to
+automatically ensure checks have to pass before committing.
+
+Once all `pre-commit` checks have passed (or you need help),
+please commit your changes with short and clear messages.
+
+
+# Reporting a bug
+
+## Security disclosures
+
+If you find a security vulnerability, please do not open an
+issue. Email adrien.wehrle@hotmail.fr instead.
+
+In order to determine whether you are dealing with a security issue,
+ask yourself these two questions:
+
+- Can I access something that's not mine, or something I shouldn't
+  have access to?
+- Can I disable something for other people?
+
+## How to file a bug report
+
+When filing an issue at
+[earthspy/issues](https://github.com/AdrienWehrle/earthspy/issues),
+make sure to answer these five questions:
+
+- Have you installed `earthspy` using
+  [`environment.yml`](https://github.com/AdrienWehrle/earthspy/blob/main/LICENSE)?
+  If not, what version of Python and dependencies are you using?
+- What operating system and processor architecture are you using?
+- What did you do?
+- What did you expect to see?
+- What did you see instead?
+
+
+# Rights
+
+The license (see
+[`LICENSE`](https://github.com/AdrienWehrle/earthspy/blob/main/LICENSE))
+applies to all contributions.
+
+# Credits
+
+Part of this document is based on [nayafia](https://github.com/nayafia)'s [CONTRIBUTING](https://github.com/nayafia) template and [geoutils CONTRIBUTING](https://github.com/GlacioHack/geoutils/blob/main/CONTRIBUTING.md).
diff --git a/CONTRIBUTING.org b/CONTRIBUTING.org
deleted file mode 100644
index d2cde9f..0000000
--- a/CONTRIBUTING.org
+++ /dev/null
@@ -1,131 +0,0 @@
-* Introduction
-
-First off, thank you for considering contributing to =earthspy=! 😊
-
-Following the guidelines presented here helps to communicate that you
-respect the efforts the developers managing and developing this open
-source project have put to foster community development. In return,
-they should reciprocate that respect in addressing your issue,
-assessing changes, and helping you finalize your pull requests. 🌻
-
-Any kind of contribution is more than welcome. Improving
-documentation, bug triaging, implementing new features or writing
-tutorials are all examples of helpful contributions. 🚀
-
-* Making a contribution
-
-** Overview
-
- 1. Fork =AdrienWehrle/earthspy= and clone your fork repository locally.
- 2. Set up the development environment (section below).
- 3. Create a branch for the new feature or bug fix.
- 4. Make your changes, and add or modify related tests in =tests/=.
- 5. Commit, making sure to run pre-commit separately if not installed as git hook.
- 6. Push to your fork.
- 7. Open a pull request from GitHub to discuss and eventually merge.
-
-
-** Step by step
-
-*** Setup
-
-Clone the git repository and create a [[https://docs.conda.io/projects/conda/en/latest/index.html][conda]] or [[https://mamba.readthedocs.io/en/latest/index.html][mamba]] environment. If
-you use mamba (mamba is great), just replace =conda= for =mamba=
-below. Steps below are similar to those presented in the [[https://github.com/AdrienWehrle/earthspy/tree/main][README]] except
-=dev-environment.yml= is used here instead of =environment.yml= as it
-contains necessary dependencies for continuous integration and
-continuous development.
-
-#+begin_src shell :results verbatim
-
-# clone repository
-git clone git@github.com:AdrienWehrle/earthspy.git
-
-# move into earthspy directory
-cd earthspy
-
-# create conda environment
-conda env create -f dev-environment.yml
-
-# activate conda environment
-conda activate earthspy-dev
-
-# install earthspy
-pip install -e .
-
-#+end_src
-
-*** Tests
-
-If your PR targets the implementation of a new feature or the
-improvement of existing ones, please add at least one test per feature
-(in the associated =tests/test_earthspy.py= file) and include them in
-your PR, using =pytests= (see existing tests for examples).
-
-To run the entire test suite, run pytest in the current directory:
-
-#+begin_src shell :results verbatim
-pytest
-#+end_src
-
-
-*** Formatting and linting
-
-Before you make your commit, please install =pre-commit= (see
-[[https://pre-commit.com/][pre-commit documentation]]), which will use =.pre-commit-config.yaml= to
-verify spelling errors, import sorting, type checking, formatting and
-linting.
-
-You can then run =pre-commit= manually:
-
-#+begin_src shell :results verbatim
-pre-commit run --all-files
-#+end_src
-
-In your PR, make sure to note if all =pre-commit= checks passed or
-not. Other developers will gladly help you getting rid of remaining
-red signs in your terminal if you feel stuck! 🌿
-
-Optionally, =pre-commit= can also be installed as a git hook to
-automatically ensure checks have to pass before committing.
-
-Once all =pre-commit= checks have passed (or you need help),
-please commit your changes with short and clear messages.
-
-
-* Reporting a bug
-
-** Security disclosures
-
-If you find a security vulnerability, please do not open an
-issue. Email adrien.wehrle@hotmail.fr instead.
-
-In order to determine whether you are dealing with a security issue,
-ask yourself these two questions:
-
-- Can I access something that's not mine, or something I shouldn't
-  have access to?
-- Can I disable something for other people?
-
-** How to file a bug report
-
-When filing an issue at
-[[earthspy/issues][https://github.com/AdrienWehrle/earthspy/issues]], make sure to answer
-these five questions:
-
-- Have you installed =earthspy= using =environment.yml=? If not, what
-  version of Python and dependencies are you using?
-- What operating system and processor architecture are you using?
-- What did you do?
-- What did you expect to see?
-- What did you see instead?
-
-
-* Rights
-
-The license (see =LICENSE=) applies to all contributions.
-
-* Credits
-
-Part of this document is based on [[https://github.com/nayafia][nayafia]]'s [[https://github.com/nayafia/contributing-template/blob/master/CONTRIBUTING-template.md][CONTRIBUTING]] template and
-[[https://github.com/GlacioHack/geoutils/blob/main/CONTRIBUTING.md][geoutils CONTRIBUTING]].
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..6b3f482
--- /dev/null
+++ b/README.md
@@ -0,0 +1,167 @@
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![Continuous integration](https://github.com/AdrienWehrle/earthspy/workflows/CI/badge.svg)](https://github.com/AdrienWehrle/earthspy/actions)
+[![CodeQL](https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml/badge.svg)](https://github.com/AdrienWehrle/earthspy/actions/workflows/codeql.yml)
+[![readthedocs](https://readthedocs.org/projects/earthspy/badge/?version=latest)]()
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://pre-commit.com/)
+[![codecov](https://codecov.io/gh/AdrienWehrle/earthspy/branch/main/graph/badge.svg)](https://codecov.io/gh/AdrienWehrle/earthspy)
+[![black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+
+
+# earthspy 🛰️ :earth_africa: :earth_americas: :earth_asia:
+
+`earthspy` is a wrapper around methods for the download of satellite data offered in the [sentinelhub-py Python package](https://github.com/sentinel-hub/sentinelhub-py). This tool makes the monitoring and study of any place on Earth simple, ready to use and easily deployable for operational purposes and automated Near-Real Time (NRT) applications.
+
+Some useful capabilities:
+  - Data download in multiprocessing
+  - Data download at optimized resolutions with the Direct (D) download mode
+  - Data download at native resolutions with the Split and Merge (SM) downlodad mode
+  - Data storage with efficient structure and file naming
+
+As `earthspy` is built on top of the [Sentinel Hub services](https://www.sentinel-hub.com/), it includes e.g. the data pre-processing through [custom scripts](https://docs.sentinel-hub.com/api/latest/evalscript/) allowing the user to process and download only the products needed (such as high-level indices) therefore optimizing download time and local storage.
+
+#  Table of Contents
+- [earthspy](#earthspy-%EF%B8%8F-earth_africa-earth_americas-earth_asia)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Operational Near Real-Time (NRT) deployment](#operational-near-real-time-nrt-deployment)
+- [Documentation](#documentation)
+- [Contributing](#contributing)
+
+# Installation
+
+It is recommended to install `earthspy` via [Github](https://github.com/), with [conda](https://docs.conda.io/en/latest/) and [pip](https://pip.pypa.io/en/stable/):
+
+```bash
+
+# clone repository
+git clone git@github.com:AdrienWehrle/earthspy.git
+
+# move into earthspy directory
+cd earthspy
+
+# create conda environment
+conda env create -f environment.yml
+
+# activate conda environment
+conda activate earthspy
+
+# install earthspy
+pip install -e .
+```
+
+- Using `pip` together with `conda` is usually a bad idea, but here `conda` installs all the dependencies and `pip` only sets up the associated paths, that's all! :+1:
+- Installation can be sped up using the fast cross-platform package manager [mamba](https://mamba.readthedocs.io/en/latest/) (reimplementation of the conda package manager in C++), simply use `mamba` instead of `conda` in the instructions above!
+
+
+# Usage
+At present `earthspy` can be run within a couple of lines of Python code that execute three main tasks:
+- set up a Sentinel Hub connection (for a given Sentinel Hub account)
+- set query parameters including Sentinel Hub API variables and `earthspy` additional ones (mainly for download efficiency)
+- send request
+
+Below is presented a simple application of `earthspy` for the download of Sentinel-2 data download around Ilulissat, Greenland for a few days in August 2019 using a True Color custom script available on Sentinel Hub's [custom script online repository](https://custom-scripts.sentinel-hub.com). All other available data collections can be found [here](https://sentinelhub-py.readthedocs.io/en/latest/examples/data_collections.html).
+
+```python
+import earthspy.earthspy as es
+
+# auth.txt should contain username and password (first and second row)
+job = es.EarthSpy("/path/to/auth.txt")
+
+# as simple as it gets
+job.set_query_parameters(
+    bounding_box=[
+        -51.13,
+        69.204,
+        -51.06,
+        69.225,
+    ],  # format from doc: [min_x, min_y, max_x, max_y]
+    time_interval=["2019-08-03", "2019-08-10"],
+    evaluation_script="https://custom-scripts.sentinel-hub.com/custom-scripts/sentinel-2/true_color/script.js",
+    data_collection="SENTINEL2_L2A",
+)
+
+# and off it goes!
+job.send_sentinelhub_requests()
+```
+
+Homemade custom evalscripts can also be passed without effort to e.g. compute high-level indices (NDVI, NDSI...).
+Below is presented an example with the default evaluation script used above (to keep it short):
+
+```python
+import earthspy.earthspy as es
+
+# Sentinel-2 default True Color script
+example_evalscript = """
+    //VERSION=3
+    function setup(){
+      return{
+        input: ["B02", "B03", "B04", "dataMask"],
+        output: {bands: 4}
+      }
+    }
+
+    function evaluatePixel(sample){
+      // Set gain for visualisation
+      let gain = 2.5;
+      // Return RGB
+      return [sample.B04 * gain, sample.B03 * gain, sample.B02 * gain, sample.dataMask];
+    }
+
+    """
+
+# auth.txt should contain username and password (first and second row)
+job = es.EarthSpy("/path/to/auth.txt")
+
+# pass string to evaluation_script
+job.set_query_parameters(
+    bounding_box=[-51.13, 69.204, -51.06, 69.225],
+    time_interval=["2019-08-03", "2019-08-10"],
+    evaluation_script=example_evalscript,
+    data_collection="SENTINEL2_L2A",
+)
+
+# and off it goes!
+job.send_sentinelhub_requests()
+```
+
+[GEOJSON](https://geojson.org/) files containing a polygon corresponding to a given region of interest
+and its associated name can also be created at [geojson.io](https://geojson.io/#map=2/20.0/0.0) and stored in [`./data`](https://github.com/AdrienWehrle/earthspy/tree/main/data).
+In this way, the name of the region can be directly passed to the `bounding_box`
+query parameter. See below for a simple example with the [ilulissat.geojson](https://github.com/AdrienWehrle/earthspy/tree/main/data/ilulissat.geojson) example file.
+
+```python
+import earthspy.earthspy as es
+
+# auth.txt should contain username and password (first and second row)
+job = es.EarthSpy("/path/to/auth.txt")
+
+# as simple as it gets
+job.set_query_parameters(
+    bounding_box="Ilulissat",
+    time_interval=["2019-08-03", "2019-08-10"],
+    evaluation_script="https://custom-scripts.sentinel-hub.com/custom-scripts/sentinel-2/true_color/script.js",
+    data_collection="SENTINEL2_L2A",
+)
+
+# and off it goes!
+job.send_sentinelhub_requests()
+```
+
+
+# Operational Near Real-Time (NRT) deployment
+
+`earthspy` can be easily deployed for NRT monitoring. The setup is as simple as wrapping the query parameters in a short python script such as [earthspy_NRT.py](https://github.com/AdrienWehrle/earthspy/blob/main/earthspy/operational/earthspy_NRT.py) and including it in a cron job. See an example below where Sentinel-2 images of Ilulissat, Greenland acquired over the past three days are downloaded everyday at noon.
+```bash
+# m h  dom mon dow   command
+00 12 * * * /bin/bash -c "/path/to/earthspy_NRT.py" > /path/to/log/log_earthspy_NRT.txt
+```
+
+# Documentation
+
+The documentation of `earthspy` is hosted on [readthedocs](https://earthspy.readthedocs.io/en/latest/).
+
+# Contributing
+
+Contributions to `earthspy` are more than welcome! Guidelines are
+presented in [CONTRIBUTING.md](https://github.com/AdrienWehrle/earthspy/blob/main/CONTRIBUTING.md).

From 07967b4f6d8b9b5c2666686560f5f9f48b6d43de Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 20:47:56 +0100
Subject: [PATCH 13/13] Bump github/super-linter from 5.0.0 to 7 (#117)

Bumps [github/super-linter](https://github.com/github/super-linter) from 5.0.0 to 7.
- [Release notes](https://github.com/github/super-linter/releases)
- [Changelog](https://github.com/github/super-linter/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/super-linter/compare/v5.0.0...v7)

---
updated-dependencies:
- dependency-name: github/super-linter
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bf53d1b..1ae9a63 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,7 +36,7 @@ jobs:
           fetch-depth: 0
 
       - name: Lint code base
-        uses: github/super-linter/slim@v5.0.0
+        uses: github/super-linter/slim@v7
         env:
           VALIDATE_ALL_CODEBASE: true
           VALIDATE_JSON: true