Migrate to no longer use SEP and use astropy Photutils instead.

.github/workflows/build-docker.yml

@@ -0,0 +1,58 @@
+name: Docker Image
+
+concurrency: ${{ github.workflow }}-${{ github.ref }}
+
+on:
+  push:
+    branches:
+      - "*"
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build-push:
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      packages: write
+
+    env:
+      REGISTRY: ghcr.io
+      IMAGE_NAME: ${{ github.repository }}
+
+    steps:
+      - name: "Checkout"
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          install: true
+
+      - name: Login to Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and also push Dockerimage
+        id: build-and-push
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

CHANGES.md

@@ -1,3 +1,7 @@
+1.13.0 (2023-10-05)
+-------------------
+- Migrated photometry extraction to be done by astropy's photutils instead of SEP.
+
 1.12.0 (2023-08-10)
 -------------------
 - Added the process_by_group keyword to stages to fix a bug that wouldn't allow grouping only by instrument

Dockerfile

@@ -1,26 +1,26 @@
-FROM continuumio/miniconda3:4.10.3
+FROM continuumio/miniconda3:23.5.2-0
 
-RUN conda install -y numpy pip scipy astropy pytest mock requests ipython coverage pyyaml\
-        && conda install -y -c conda-forge kombu=4.4.0 elasticsearch\<6.0.0,\>=5.0.0 pytest-astropy mysql-connector-python\
-        && conda clean -y --all
-
-RUN pip install --no-cache-dir cython logutils lcogt_logging python-dateutil sqlalchemy\>=1.3.0b1 psycopg2-binary celery[redis]==4.3.0 \
-        apscheduler ocs-ingester tenacity amqp==2.6.0 cosmic-conn
+#  In principle I could remove the gcc to shrink the image, but pytorch is already so large it doesn't make much difference
+RUN apt-get -y update && apt-get -y install gcc && \
+        apt-get autoclean && \
+        rm -rf /var/lib/apt/lists/*
 
 RUN mkdir /home/archive && /usr/sbin/groupadd -g 10000 "domainusers" \
         && /usr/sbin/useradd -g 10000 -d /home/archive -M -N -u 10087 archive \
         && chown -R archive:domainusers /home/archive
 
-COPY --chown=10087:10000 . /lco/banzai
-
-RUN apt-get -y update && apt-get -y install gcc && \
-        pip install --no-cache-dir git+https://github.com/cmccully/sep.git@deblending /lco/banzai/ && \
-        apt-get -y remove gcc && \
-        apt-get autoclean && \
-        rm -rf /var/lib/apt/lists/*
-
 USER archive
 
 ENV HOME /home/archive
 
 WORKDIR /home/archive
+
+COPY environment.yaml .
+
+RUN  . /opt/conda/etc/profile.d/conda.sh && conda env create -p /home/archive/envs/banzai -f environment.yaml --solver=libmamba
+
+COPY --chown=10087:10000 . /lco/banzai
+
+ENV PATH /home/archive/envs/banzai/bin:$PATH
+
+RUN /home/archive/envs/banzai/bin/pip install --no-cache-dir /lco/banzai/ 

banzai/bpm.py

@@ -39,6 +39,6 @@ def calibration_type(self):
 class SaturatedPixelFlagger(Stage):
     def do_stage(self, image):
         for image_extension in image.ccd_hdus:
-            image_extension.mask[image_extension.data > image_extension.saturate] |= 2
+            image_extension.mask[image_extension.data >= image_extension.saturate] |= 2
 
         return image