From 1163a67b6b6126f67f22720062c8531d4b1330ec Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Tue, 23 Aug 2022 13:27:45 +0200
Subject: [PATCH 01/11] Update utils.py

---
 kafka/inference/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/kafka/inference/utils.py b/kafka/inference/utils.py
index 1a43e4b..0d6e313 100644
--- a/kafka/inference/utils.py
+++ b/kafka/inference/utils.py
@@ -32,7 +32,10 @@
 import scipy.sparse.linalg as spl
 import datetime as dt
 import os
-import gdal
+try:
+    from osgeo import gdal
+except ImportError:
+    import gdal
 
 import logging
 LOG = logging.getLogger(__name__)

From a28f4da4a722a76b392d9bb50252623eaa5c42c5 Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Tue, 23 Aug 2022 13:28:35 +0200
Subject: [PATCH 02/11] Update Sentinel1_Observations.py

---
 kafka/input_output/Sentinel1_Observations.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/kafka/input_output/Sentinel1_Observations.py b/kafka/input_output/Sentinel1_Observations.py
index e9107d6..b4cedcf 100644
--- a/kafka/input_output/Sentinel1_Observations.py
+++ b/kafka/input_output/Sentinel1_Observations.py
@@ -7,11 +7,17 @@
 import os
 from collections import namedtuple
 
-import gdal
+try:
+    from osgeo import gdal
+except ImportError:
+    import gdal
 
 import numpy as np
 
-import osr
+try:
+    from osgeo import osr
+except ImportError:
+    import osr
 
 import scipy.sparse as sp
 

From 5fc28578dba2f925e973c53390a858beab9e3f2f Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Tue, 23 Aug 2022 13:29:08 +0200
Subject: [PATCH 03/11] Update Sentinel2_Observations.py

---
 kafka/input_output/Sentinel2_Observations.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/kafka/input_output/Sentinel2_Observations.py b/kafka/input_output/Sentinel2_Observations.py
index 71c889d..a0bc816 100644
--- a/kafka/input_output/Sentinel2_Observations.py
+++ b/kafka/input_output/Sentinel2_Observations.py
@@ -7,8 +7,15 @@
 
 import numpy as np
 import scipy.sparse as sp # Required for unc
-import gdal
-import osr
+try:
+    from osgeo import gdal
+except ImportError:
+    import gdal
+
+try:
+    from osgeo import osr
+except ImportError:
+    import osr
 
 import xml.etree.ElementTree as ET
 from collections import namedtuple

From 9ec2d452844f3512c9c7568e4de9921ff34f9826 Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Tue, 23 Aug 2022 13:29:45 +0200
Subject: [PATCH 04/11] Update observations.py

---
 kafka/input_output/observations.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/kafka/input_output/observations.py b/kafka/input_output/observations.py
index d0b25ba..4affd32 100644
--- a/kafka/input_output/observations.py
+++ b/kafka/input_output/observations.py
@@ -46,7 +46,12 @@
 
 from BRDF_descriptors import RetrieveBRDFDescriptors
 
-import gdal
+
+try:
+    from osgeo import gdal
+except ImportError:
+    import gdal
+
 
 import numpy as np
 #  from kernels import Kernels

From 8d1fc44740e9a5704f65b973f0370cc4c9cd8922 Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Tue, 23 Aug 2022 13:30:27 +0200
Subject: [PATCH 05/11] Update utils.py

---
 kafka/input_output/utils.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/kafka/input_output/utils.py b/kafka/input_output/utils.py
index d138f9e..8222b5b 100644
--- a/kafka/input_output/utils.py
+++ b/kafka/input_output/utils.py
@@ -1,6 +1,16 @@
 import numpy as np
-import gdal
-import osr
+
+try:
+    from osgeo import gdal
+except ImportError:
+    import gdal
+
+try:
+    from osgeo import osr
+except ImportError:
+    import osr
+
+    
 """
 I need to put some utils in here. Seems like the most obvious place...
 """

From d817d112317da2a7a06fd9a33b3d9e6b2b3e3154 Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Thu, 12 Jan 2023 14:52:06 +0100
Subject: [PATCH 06/11] Update setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index c2a3ed1..4129652 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
     'numpy',
     'scipy',
     'gdal',
-    # 'BRDF_descriptors', # Not available for automatic installation
+    'BRDF_descriptors @ https://github.com/QCDIS/BRDF_descriptors.git',
     'matplotlib'
 ]
 

From bb9a734dca9b469a36feba36fb1d335764fca4c3 Mon Sep 17 00:00:00 2001
From: skoulouzis <skoulouzis@users.noreply.github.com>
Date: Thu, 12 Jan 2023 22:34:29 +0100
Subject: [PATCH 07/11] Update setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4129652..81557fd 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
     'numpy',
     'scipy',
     'gdal',
-    'BRDF_descriptors @ https://github.com/QCDIS/BRDF_descriptors.git',
+    'BRDF_descriptors',
     'matplotlib'
 ]
 

From 3a31d0df5c112c6ed4bde09054a5298fb05f6329 Mon Sep 17 00:00:00 2001
From: skoulouzis <koulouzis@gmail.com>
Date: Tue, 21 Mar 2023 14:22:05 +0100
Subject: [PATCH 08/11] update dependencies

---
 .github/workflows/run-tests.yml    | 38 ++++++++++++++++++++++++++++++
 environment.yml                    | 35 +++++++++++++++++++++++++++
 kafka/inference/utils.py           |  2 +-
 kafka/input_output/observations.py |  9 ++++---
 kafka/linear_kf.py                 | 18 +++++---------
 setup.py                           |  8 +------
 6 files changed, 85 insertions(+), 25 deletions(-)
 create mode 100644 .github/workflows/run-tests.yml
 create mode 100644 environment.yml

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
new file mode 100644
index 0000000..be0667a
--- /dev/null
+++ b/.github/workflows/run-tests.yml
@@ -0,0 +1,38 @@
+name: make
+on:
+  pull_request:
+  push:
+  schedule:
+    - cron: '0 0 2 * *'
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      max-parallel: 5
+      matrix:
+        environment_file: [environment.yml]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+
+    - name: Install dependencies
+      run: |
+        conda env update --file ${{ matrix.environment_file }} --name base
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..de7c55a
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,35 @@
+name: multiply-KaFKA-inference-engine
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=>3.8
+  - gdal=2.4
+  - libgdal
+  - pyproj
+  - sentinelhub
+  - pyyaml
+  - numpy
+  - scipy
+  - setuptools
+  - gcc=12.1.0
+  - cxx-compiler
+  - matplotlib
+  - libgcc
+  - libstdcxx-ng
+  - lazrs-python
+  - laspy
+  - pyyaml
+  - setuptools
+  - pytest
+  - flake8
+  - scipy
+  - shapely
+  - pytest-shutil
+  - pip
+  - pip:
+      - .
+      - git+https://github.com/QCDIS/BRDF_descriptors.git
+      - git+https://github.com/QCDIS/atmospheric_correction.git
diff --git a/kafka/inference/utils.py b/kafka/inference/utils.py
index 0d6e313..75c470a 100644
--- a/kafka/inference/utils.py
+++ b/kafka/inference/utils.py
@@ -343,7 +343,7 @@ def spsolve2(a, b):
     a_lu = spl.splu(a.tocsc())   # LU decomposition for sparse a
     out = sp.lil_matrix((a.shape[1], b.shape[1]), dtype=np.float32)
     b_csc = b.tocsc()
-    for j in xrange(b.shape[1]):
+    for j in range(b.shape[1]):
         bb = np.array(b_csc[j, :].todense()).squeeze()
         out[j, j] = a_lu.solve(bb)[j]
     return out.tocsr()
diff --git a/kafka/input_output/observations.py b/kafka/input_output/observations.py
index 4affd32..28cf233 100644
--- a/kafka/input_output/observations.py
+++ b/kafka/input_output/observations.py
@@ -38,23 +38,22 @@
 MCD43A1/2 -> See BRDF_descriptors!
 
 """
-import datetime
 import _pickle as cPickle
+import datetime
 import glob
 import os
 from collections import namedtuple
 
 from BRDF_descriptors import RetrieveBRDFDescriptors
 
-
 try:
     from osgeo import gdal
 except ImportError:
     import gdal
 
+from SIAC import  kernels
 
 import numpy as np
-#  from kernels import Kernels
 
 import scipy.sparse as sp
 from scipy.ndimage import zoom
@@ -139,7 +138,7 @@ def get_band_data(self, the_date, band_no):
         vza = zoom(vza, 2, order=0)
         sza = zoom(sza, 2, order=0)
         mask = zoom(mask, 2, order=0)
-        K = Kernels(vza, sza, raa, LiType="Sparse", doIntegrals=False,
+        K = kernels.Kernels(vza, sza, raa, LiType="Sparse", doIntegrals=False,
                     normalise=1, RecipFlag=True,
                     RossHS=False, MODISSPARSE=True, RossType="Thick")
         uncertainty = refl*0 + unc[band_no-1]
@@ -195,7 +194,7 @@ def get_band_data(self, the_date, band_no):
         # find the requested date
         date_idx = self.dates.index(the_date)
         BHR = []
-        for band in xrange(7):
+        for band in range(7):
             g = gdal.Open(self.kernels[date_idx].replace(
                 "b0", "b%d" % band))
             kernels = g.ReadAsArray()  # 3*nx*ny
diff --git a/kafka/linear_kf.py b/kafka/linear_kf.py
index 15c20ff..72b8a82 100644
--- a/kafka/linear_kf.py
+++ b/kafka/linear_kf.py
@@ -24,24 +24,18 @@
 from collections import namedtuple
 
 import numpy as np
-
 import scipy.sparse as sp
 
-# from scipy.spatial.distance import squareform, pdist
-
-# from utils import  matrix_squeeze, spsolve2, reconstruct_array
-
+from .inference import hessian_correction
+from .inference import iterate_time_grid
+from .inference import propagate_information_filter_LAI  # eg
 from .inference import variational_kalman
 from .inference import variational_kalman_multiband
-from .inference import locate_in_lut, run_emulator, create_uncertainty
-from .inference import create_linear_observation_operator
-from .inference import create_nonlinear_observation_operator
-from .inference import iterate_time_grid
-from .inference import propagate_information_filter_LAI # eg
-from .inference import hessian_correction
-from .inference import hessian_correction_multiband
 from .inference.kf_tools import propagate_and_blend_prior
 
+# from scipy.spatial.distance import squareform, pdist
+# from utils import  matrix_squeeze, spsolve2, reconstruct_array
+
 # Set up logging
 
 LOG = logging.getLogger(__name__+".linear_kf")
diff --git a/setup.py b/setup.py
index c2a3ed1..2fe526f 100644
--- a/setup.py
+++ b/setup.py
@@ -3,12 +3,6 @@
 from setuptools import setup, find_packages
 
 requirements = [
-    'pytest',
-    'numpy',
-    'scipy',
-    'gdal',
-    # 'BRDF_descriptors', # Not available for automatic installation
-    'matplotlib'
 ]
 
 setup(name='KaFKA',
@@ -16,4 +10,4 @@
       author='MULTIPLY Team',
       packages=find_packages(),
       install_requires=requirements
-)
+      )

From b922bb968ac03e30bbd4465365a85382e23b5569 Mon Sep 17 00:00:00 2001
From: skoulouzis <koulouzis@gmail.com>
Date: Sun, 30 Apr 2023 12:23:03 +0200
Subject: [PATCH 09/11] added sync

---
 .github/workflows/git-sync.yml | 43 ++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 .github/workflows/git-sync.yml

diff --git a/.github/workflows/git-sync.yml b/.github/workflows/git-sync.yml
new file mode 100644
index 0000000..b3d1267
--- /dev/null
+++ b/.github/workflows/git-sync.yml
@@ -0,0 +1,43 @@
+name: Sync with Original Repo
+on:
+  schedule:
+  - cron:  "0 0 * * Sun"
+
+
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Fetch upstream
+      run: |
+        git remote add upstream https://github.com/QCDIS/KaFKA-InferenceEngine.git
+        git fetch upstream
+
+    - name: Check if there are changes
+      id: has_changes
+      run: echo "::set-output name=changed::$(git rev-parse HEAD != upstream/master)"
+
+    - name: Create new branch
+      run: |
+        git checkout -b update-upstream-${{ github.run_number }}
+      if: steps.has_changes.outputs.changed == 'true'
+      
+    - name: Merge upstream changes
+      run: |
+        git merge upstream/master --no-edit
+      if: steps.has_changes.outputs.changed == 'true'
+
+    - name: Create pull request
+      uses: peter-evans/create-pull-request@v3
+      if: steps.has_changes.outputs.changed == 'true'
+      with:
+        title: 'Update from upstream repository'
+        commit-message: 'Merge latest changes from upstream repository'
+        branch: 'update-upstream'
+        base: 'master'
+        delete-branch: true

From 1fde76d5843c3ab423ea48b988b3cc3b5b2608b5 Mon Sep 17 00:00:00 2001
From: skoulouzis <koulouzis@gmail.com>
Date: Sun, 30 Apr 2023 12:24:05 +0200
Subject: [PATCH 10/11] added sync

---
 .github/workflows/git-sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/git-sync.yml b/.github/workflows/git-sync.yml
index b3d1267..d1fca96 100644
--- a/.github/workflows/git-sync.yml
+++ b/.github/workflows/git-sync.yml
@@ -15,7 +15,7 @@ jobs:
 
     - name: Fetch upstream
       run: |
-        git remote add upstream https://github.com/QCDIS/KaFKA-InferenceEngine.git
+        git remote add upstream https://github.com/multiply-org/KaFKA-InferenceEngine.git
         git fetch upstream
 
     - name: Check if there are changes

From 658bbe1cfef1ee10df52fe75d4fdc7021bc40924 Mon Sep 17 00:00:00 2001
From: skoulouzis <koulouzis@gmail.com>
Date: Sun, 30 Apr 2023 23:48:43 +0200
Subject: [PATCH 11/11] fix F821 undefined name 'ogr'

---
 kafka/input_output/utils.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/kafka/input_output/utils.py b/kafka/input_output/utils.py
index 8222b5b..827f396 100644
--- a/kafka/input_output/utils.py
+++ b/kafka/input_output/utils.py
@@ -1,15 +1,8 @@
-import numpy as np
-
 try:
-    from osgeo import gdal
+    from osgeo import gdal, ogr, osr
 except ImportError:
     import gdal
-
-try:
-    from osgeo import osr
-except ImportError:
     import osr
-
     
 """
 I need to put some utils in here. Seems like the most obvious place...