From 044be7bc69e931f39156971c184eed454a522898 Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 10:59:49 +1100
Subject: [PATCH 1/7] Create run-pytest.yml

---
 .github/workflows/run-pytest.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/workflows/run-pytest.yml

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
new file mode 100644
index 0000000..3029095
--- /dev/null
+++ b/.github/workflows/run-pytest.yml
@@ -0,0 +1,21 @@
+name: Run Tests with Pytest
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  create-environment:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: mamba-org/setup-micromamba@v2.0.3
+      with:
+        generate-run-shell: true
+        environment-name: test-env
+        create-args: >-
+          python=3.10
+          pytest
+    - shell: micromamba-shell {0}
+    - run: |
+        pytest --version

From e131e4c30508de4a8d0539a6b440fefcae95b13b Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 11:03:37 +1100
Subject: [PATCH 2/7] change syntax of shell + run

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

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 3029095..a505774 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -17,5 +17,5 @@ jobs:
           python=3.10
           pytest
     - shell: micromamba-shell {0}
-    - run: |
+      run: |
         pytest --version

From e9632e5b52387ad4420edd32db198f4b8c21d0b8 Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 11:50:32 +1100
Subject: [PATCH 3/7] Update workflow to use environment file

---
 .github/workflows/run-pytest.yml | 21 ++++++++++++++-------
 test_environment.yml             | 10 ++++++++++
 2 files changed, 24 insertions(+), 7 deletions(-)
 create mode 100644 test_environment.yml

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index a505774..57af321 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -5,17 +5,24 @@ on:
     branches: [main]
 
 jobs:
-  create-environment:
+  run-tests:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: mamba-org/setup-micromamba@v2.0.3
+    - name: Set up micromamba environment
+      uses: mamba-org/setup-micromamba@v2.0.3
       with:
         generate-run-shell: true
-        environment-name: test-env
-        create-args: >-
-          python=3.10
-          pytest
-    - shell: micromamba-shell {0}
+        environment-file: test_environment.yml
+        condarc: |
+        channels:
+          - conda-forge
+    - name: Check packages
+      shell: micromamba-shell {0}
       run: |
+        python --version
         pytest --version
+    - name: Run tests
+      shell: micromamba-shell {0}
+      run: |
+        pytest
diff --git a/test_environment.yml b/test_environment.yml
new file mode 100644
index 0000000..b4c4ac0
--- /dev/null
+++ b/test_environment.yml
@@ -0,0 +1,10 @@
+name: test-env
+dependencies:
+  - python=3.10.16=he725a3c_1_cpython
+  - gdal=3.10.0=py310h79127d3_13
+  - shapely=2.0.6=py310had3dfd6_2
+  - pip=24.3.1=pyh8b19718_2
+  - pip:
+    - click==8.1.8
+    - pytest==8.3.4
+    - .
\ No newline at end of file

From c1bcbf273d633aba43e364f2eeb8e0e88c39acf6 Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 11:53:41 +1100
Subject: [PATCH 4/7] Fix formatting for condarc

---
 .github/workflows/run-pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 57af321..2c98c86 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -15,8 +15,8 @@ jobs:
         generate-run-shell: true
         environment-file: test_environment.yml
         condarc: |
-        channels:
-          - conda-forge
+          channels:
+            - conda-forge
     - name: Check packages
       shell: micromamba-shell {0}
       run: |

From c67ecde491a2493557f2207c8173bf9eab8fa4a7 Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 12:30:26 +1100
Subject: [PATCH 5/7] Update environment.yml file

---
 environment.yml      | 293 +++++++++----------------------------------
 test_environment.yml |  10 --
 2 files changed, 60 insertions(+), 243 deletions(-)
 delete mode 100644 test_environment.yml

diff --git a/environment.yml b/environment.yml
index be4ad55..747e812 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,265 +1,92 @@
 name: sar-antarctica
 channels:
   - conda-forge
-  - defaults
 dependencies:
-  - affine=2.4.0
-  - appnope=0.1.4
-  - argon2-cffi=23.1.0
-  - argon2-cffi-bindings=21.2.0
-  - arrow=1.3.0
-  - asttokens=2.4.1
-  - attrs=23.2.0
-  - aws-c-auth=0.7.22
-  - aws-c-cal=0.6.15
-  - aws-c-common=0.9.19
-  - aws-c-compression=0.2.18
-  - aws-c-event-stream=0.4.2
-  - aws-c-http=0.8.2
-  - aws-c-io=0.14.9
-  - aws-c-mqtt=0.10.4
-  - aws-c-s3=0.5.10
-  - aws-c-sdkutils=0.1.16
-  - aws-checksums=0.1.18
-  - aws-crt-cpp=0.26.12
-  - aws-sdk-cpp=1.11.329
-  - azure-core-cpp=1.12.0
-  - azure-identity-cpp=1.8.0
-  - azure-storage-blobs-cpp=12.11.0
-  - azure-storage-common-cpp=12.6.0
-  - babel=2.14.0
-  - bcrypt=4.1.3
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - aom=3.9.1
   - blosc=1.21.6
-  - brotli=1.1.0
-  - brotli-bin=1.1.0
-  - brotli-python=1.1.0
   - bzip2=1.0.8
-  - c-ares=1.28.1
-  - ca-certificates=2024.6.2
-  - cairo=1.18.0
-  - certifi=2024.6.2
-  - cffi=1.16.0
-  - cfitsio=4.4.0
-  - charset-normalizer=3.3.2
-  - click=8.1.7
-  - click-plugins=1.1.1
-  - cligj=0.7.2
-  - colour=0.1.5
-  - comm=0.2.2
-  - contourpy=1.2.1
-  - cryptography=42.0.8
-  - cycler=0.12.1
-  - debugpy=1.8.1
-  - decorator=5.1.1
-  - dill=0.3.8
-  - exceptiongroup=1.2.0
-  - executing=2.0.1
-  - expat=2.6.2
-  - fmt=10.2.1
-  - font-ttf-dejavu-sans-mono=2.37
-  - font-ttf-inconsolata=3.000
-  - font-ttf-source-code-pro=2.038
-  - font-ttf-ubuntu=0.83
-  - fontconfig=2.14.2
-  - fonts-conda-ecosystem=1
-  - fonts-conda-forge=1
-  - fonttools=4.53.0
-  - freetype=2.12.1
+  - c-ares=1.34.4
+  - ca-certificates=2024.12.14
+  - dav1d=1.2.1
   - freexl=2.0.0
-  - furl=2.1.3
-  - gdal=3.9.0
-  - geoalchemy2=0.13.3
-  - geos=3.12.1
+  - gdal=3.10.0
+  - geos=3.13.0
   - geotiff=1.7.3
   - giflib=5.2.2
-  - greenlet=3.0.3
-  - hdf4=4.2.15
-  - hdf5=1.14.3
-  - icu=73.2
-  - idna=3.7
-  - importlib-metadata=7.2.1
-  - importlib_metadata=7.2.1
-  - infinity=1.5
-  - intervals=0.9.2
-  - ipykernel=6.29.4
-  - ipython=8.25.0
-  - jedi=0.19.1
-  - json-c=0.17
-  - jupyter=1.1.1
-  - jupyter_client=8.6.2
-  - jupyter_core=5.7.2
-  - kealib=1.5.3
-  - kiwisolver=1.4.5
-  - krb5=1.21.2
-  - lcms2=2.16
+  - icu=75.1
+  - json-c=0.18
+  - keyutils=1.6.1
+  - krb5=1.21.3
+  - ld_impl_linux-64=2.43
   - lerc=4.0.0
-  - libabseil=20240116.2
-  - libaec=1.1.3
-  - libarchive=3.7.4
+  - libarchive=3.7.7
+  - libavif16=1.1.1
   - libblas=3.9.0
-  - libboost-headers=1.85.0
-  - libbrotlicommon=1.1.0
-  - libbrotlidec=1.1.0
-  - libbrotlienc=1.1.0
   - libcblas=3.9.0
-  - libcrc32c=1.1.2
-  - libcurl=8.8.0
-  - libcxx=17.0.6
-  - libdeflate=1.20
-  - libedit=3.1.20191231
+  - libcurl=8.11.1
+  - libde265=1.0.15
+  - libdeflate=1.23
+  - libedit=3.1.20240808
   - libev=4.33
-  - libexpat=2.6.2
+  - libexpat=2.6.4
   - libffi=3.4.2
-  - libgdal=3.9.0
-  - libgfortran5=13.2.0
-  - libglib=2.80.2
-  - libgoogle-cloud=2.25.0
-  - libgoogle-cloud-storage=2.25.0
-  - libgrpc=1.62.2
+  - libgcc=14.2.0
+  - libgcc-ng=14.2.0
+  - libgdal-core=3.10.0
+  - libgfortran=14.2.0
+  - libgfortran5=14.2.0
+  - libgomp=14.2.0
+  - libheif=1.19.5
   - libiconv=1.17
   - libjpeg-turbo=3.0.0
   - libkml=1.3.0
   - liblapack=3.9.0
-  - libnetcdf=4.9.2
-  - libnghttp2=1.58.0
-  - libopenblas=0.3.27
-  - libpng=1.6.43
-  - libpq=16.3
-  - libprotobuf=4.25.3
-  - libre2-11=2023.09.01
+  - liblzma=5.6.3
+  - libnghttp2=1.64.0
+  - libnsl=2.0.1
+  - libopenblas=0.3.28
+  - libpng=1.6.45
   - librttopo=1.1.0
-  - libsodium=1.0.18
   - libspatialite=5.1.0
-  - libsqlite=3.46.0
-  - libssh2=1.11.0
-  - libtiff=4.6.0
-  - libwebp-base=1.4.0
-  - libxcb=1.16
-  - libxml2=2.12.7
-  - libxslt=1.1.39
-  - libzip=1.10.1
+  - libsqlite=3.47.2
+  - libssh2=1.11.1
+  - libstdcxx=14.2.0
+  - libstdcxx-ng=14.2.0
+  - libtiff=4.7.0
+  - libuuid=2.38.1
+  - libwebp-base=1.5.0
+  - libxcrypt=4.4.36
+  - libxml2=2.13.5
   - libzlib=1.3.1
-  - llvm-openmp=18.1.8
-  - lxml=5.2.2
-  - lz4-c=1.9.4
+  - lz4-c=1.10.0
   - lzo=2.10
-  - matplotlib-base=3.8.4
-  - matplotlib-inline=0.1.7
   - minizip=4.0.7
-  - multiprocess=0.70.16
-  - munkres=1.1.4
   - ncurses=6.5
-  - nest-asyncio=1.6.0
-  - nspr=4.35
-  - nss=3.101
-  - numpy=1.26.4
-  - openjpeg=2.5.2
-  - openssl=3.3.1
-  - orderedmultidict=1.0.1
-  - packaging=24.1
-  - parso=0.8.4
-  - passlib=1.7.4
-  - pathos=0.3.2
-  - pcre2=10.43
-  - pendulum=3.0.0
-  - pexpect=4.9.0
-  - phonenumbers=8.13.39
-  - pickleshare=0.7.5
-  - pillow=10.3.0
-  - pip=24.0
-  - platformdirs=4.2.2
-  - poppler=24.04.0
-  - poppler-data=0.4.12
-  - postgresql=16.3
-  - pox=0.3.4
-  - ppft=1.7.6.8
-  - progressbar2=4.4.2
-  - proj=9.4.1
-  - prompt-toolkit=3.0.47
-  - psutil=6.0.0
-  - psycopg2=2.9.9
-  - pthread-stubs=0.4
-  - ptyprocess=0.7.0
-  - pure_eval=0.2.2
-  - pycparser=2.22
-  - pygments=2.18.0
-  - pyparsing=3.1.2
-  - pyrosar=0.23.0
-  - pysocks=1.7.1
-  - python=3.10.14
-  - python-dateutil=2.9.0
-  - python-utils=3.8.2
+  - numpy=2.2.1
+  - openssl=3.4.0
+  - pcre2=10.44
+  - pip=24.3.1
+  - proj=9.5.1
+  - python=3.10.16
   - python_abi=3.10
-  - pytz=2024.1
-  - pyyaml=6.0.1
-  - pyzmq=26.0.3
-  - rasterio=1.3.10
-  - re2=2023.09.01
+  - rav1e=0.6.6
   - readline=8.2
-  - requests=2.32.3
-  - setuptools=70.1.0
-  - setuptools-scm=8.1.0
-  - setuptools_scm=8.1.0
-  - six=1.16.0
-  - snappy=1.2.0
-  - snuggs=1.4.7
-  - spatialist=0.13.1
-  - spdlog=1.13.0
-  - sqlalchemy=1.4.49
-  - sqlalchemy-utils=0.41.2
-  - sqlalchemy-utils-arrow=0.41.2
-  - sqlalchemy-utils-babel=0.41.2
-  - sqlalchemy-utils-base=0.41.2
-  - sqlalchemy-utils-color=0.41.2
-  - sqlalchemy-utils-encrypted=0.41.2
-  - sqlalchemy-utils-intervals=0.41.2
-  - sqlalchemy-utils-password=0.41.2
-  - sqlalchemy-utils-pendulum=0.41.2
-  - sqlalchemy-utils-phone=0.41.2
-  - sqlalchemy-utils-timezone=0.41.2
-  - sqlalchemy-utils-url=0.41.2
-  - sqlite=3.46.0
-  - stack_data=0.6.2
-  - tblib=3.0.0
-  - tiledb=2.24.1
-  - time-machine=2.14.1
+  - setuptools=75.6.0
+  - shapely=2.0.6
+  - snappy=1.2.1
+  - sqlite=3.47.2
+  - svt-av1=2.3.0
   - tk=8.6.13
-  - tomli=2.0.1
-  - tornado=6.4.1
-  - traitlets=5.14.3
-  - types-python-dateutil=2.9.0.20240316
-  - typing-extensions=4.12.2
-  - typing_extensions=4.12.2
-  - tzcode=2024a
-  - tzdata=2024a
-  - unicodedata2=15.1.0
+  - tzdata=2024b
   - uriparser=0.9.8
-  - urllib3=2.2.2
-  - wcwidth=0.2.13
-  - wheel=0.43.0
+  - wheel=0.45.1
+  - x265=3.5
   - xerces-c=3.2.5
-  - xorg-libxau=1.0.11
-  - xorg-libxdmcp=1.1.3
-  - xz=5.2.6
-  - yaml=0.2.5
-  - zeromq=4.3.5
-  - zipp=3.19.2
   - zlib=1.3.1
   - zstd=1.5.6
   - pip:
-      - asf-search==7.1.3
-      - boto3==1.34.132
-      - botocore==1.34.132
-      - ciso8601==2.3.1
-      - dateparser==1.2.0
-      - git+https://github.com/abradley60/dem-stitcher.git@dem_fill 
-      - jmespath==1.0.1
-      - pyproj==3.6.1
-      - regex==2024.5.15
-      - s3transfer==0.10.2
-      - scipy==1.14.0
-      - sentineleof==0.9.5
-      - shapely==2.0.4
-      - tenacity==8.2.2
-      - tzlocal==5.2
-      
\ No newline at end of file
+    - click==8.1.8
+    - pytest==8.3.4
+    - .
\ No newline at end of file
diff --git a/test_environment.yml b/test_environment.yml
deleted file mode 100644
index b4c4ac0..0000000
--- a/test_environment.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: test-env
-dependencies:
-  - python=3.10.16=he725a3c_1_cpython
-  - gdal=3.10.0=py310h79127d3_13
-  - shapely=2.0.6=py310had3dfd6_2
-  - pip=24.3.1=pyh8b19718_2
-  - pip:
-    - click==8.1.8
-    - pytest==8.3.4
-    - .
\ No newline at end of file

From 1bdc673b87ea3aa21c6c3b805a5e90aa7c656a9a Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 12:31:00 +1100
Subject: [PATCH 6/7] Point GitHub action to updated environment.yml file

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

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 2c98c86..93d8f1a 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -13,7 +13,7 @@ jobs:
       uses: mamba-org/setup-micromamba@v2.0.3
       with:
         generate-run-shell: true
-        environment-file: test_environment.yml
+        environment-file: environment.yml
         condarc: |
           channels:
             - conda-forge

From 7fa85548aed63abbaa6074d47f8a54ffcfe3c939 Mon Sep 17 00:00:00 2001
From: Caitlin Adams <25995927+caitlinadams@users.noreply.github.com>
Date: Thu, 9 Jan 2025 13:03:48 +1100
Subject: [PATCH 7/7] Remove channels argument -- to be handled by Actions

---
 environment.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 747e812..416aada 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,4 @@
 name: sar-antarctica
-channels:
-  - conda-forge
 dependencies:
   - _libgcc_mutex=0.1
   - _openmp_mutex=4.5