Merge pull request #21 from UBC-MDS/update-environment

Update Environment

.github/workflows/docker-publish.yml

@@ -11,6 +11,7 @@ on:
     branches:
       - main
       - create-dockerfile
+      - update-environment
     paths: 
       - 'Dockerfile'
       - 'conda-linux-64.lock'
@@ -46,3 +47,17 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Update docker-compose.yml with new image tag
+        if: success()
+        run: |
+          sed -i "s|image:  bfrizzell/mushroom_classifier:.*|image:  bfrizzell/mushroom_classifier:${{ steps.meta.outputs.version }}|" docker-compose.yml
+
+      - name: Commit and push updated docker-compose.yml
+        if: success()
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git add docker-compose.yml
+          git commit -m "Update docker-compose.yml with new image tag"
+          git push

Dockerfile

@@ -1,6 +1,17 @@
 FROM quay.io/jupyter/minimal-notebook:afe30f0c9ad8
 
+# add conda-lock
 COPY conda-linux-64.lock /tmp/conda-linux-64.lock
+
+USER root
+
+# for Quarto PDF rendering
+RUN sudo apt update \
+    && sudo apt install -y lmodern
+
+
+USER $NB_UID
+
 RUN mamba update --quiet --file /tmp/conda-linux-64.lock \
     && mamba clean --all -y -f \
     && fix-permissions "${CONDA_DIR}" \

conda-linux-64.lock

@@ -1,13 +1,16 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 396a340a2ce6fe51186ae0897e1a12987701476c202db13e2ee6c7eac4e1af0a
+# input_hash: 85e0532e36f7bcf4cc8955c51d28e77b2fef2ba2db46ede016aeb234b8d71e53
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
+https://conda.anaconda.org/conda-forge/linux-64/dart-sass-1.58.3-ha770c72_1.conda#d54982a58cd9be3d00a7efe76ba6f60c
+https://conda.anaconda.org/conda-forge/linux-64/esbuild-0.24.0-ha770c72_0.conda#b2cdfd1d3c62519b913d71f200e7f9ca
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
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 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda#8c924f0b7f3e064b1c954a08e7c32fba
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-5_cp311.conda#139a8d40c8a2f430df31048949e450de
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@@ -34,6 +37,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hb9d3cd8_1.co
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480
 https://conda.anaconda.org/conda-forge/linux-64/xorg-xorgproto-2024.1-hb9d3cd8_1.conda#7c21106b851ec72c037b162c216d8f05
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/deno-1.41.0-hfc7925d_0.conda#8d6e6bd74055bd30c88d3a678395a7e9
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.4-h5888daf_0.conda#1d6afef758879ef5ee78127eb4cd2c4a
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@@ -56,9 +60,11 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond
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+https://conda.anaconda.org/conda-forge/linux-64/typst-0.11.0-he8a937b_0.conda#f6ac8c8ab4a4c9ed0ec710e3f5fa3954
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+https://conda.anaconda.org/conda-forge/linux-64/deno-dom-0.1.35-hd9586b0_1.conda#263ee0870b18b013d9ec8539113ac69f
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@@ -89,13 +95,16 @@ https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.0-he137b08_1.conda#6
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+https://conda.anaconda.org/conda-forge/linux-64/quarto-1.5.57-ha770c72_0.conda#dd6838c663e9b5a1b18048a164ccb90b
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+https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_0.conda#454950e9fa3a0c59880de0ac7a6bc8c4
 https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292
 https://conda.anaconda.org/conda-forge/noarch/certifi-2024.8.30-pyhd8ed1ab_0.conda#12f7d00853807b0531775e9be891cb11
+https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda#f3ad426304898027fc619827ff428eca
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@@ -134,15 +143,16 @@ https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.2-pyhd8ed1ab_0.
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+https://conda.anaconda.org/conda-forge/noarch/tabulate-0.9.0-pyhd8ed1ab_1.tar.bz2#4759805cce2d914c38472f70bf4d8bcb
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-https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
-https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.13-pyhd8ed1ab_0.conda#6372cd99502721bd7499f8d16b56268d
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_1.conda#75cb7132eb58d97896e173ef12ac9986
+https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.13-pyhd8ed1ab_1.conda#237db148cc37a466e4222d589029b53e
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@@ -153,7 +163,6 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrandr-1.5.4-hb9d3cd8_0.
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-https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.1-pyhd8ed1ab_0.conda#5f25798dcefd8252ce5f9dc494d5f571
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@@ -174,30 +183,30 @@ https://conda.anaconda.org/conda-forge/noarch/plotly-5.24.1-pyhd8ed1ab_0.conda#8
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+https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.2-pyhd8ed1ab_0.conda#e7df0fdd404616638df5ece6e69ba7af
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docker-compose.yml

@@ -1,7 +1,7 @@
 services:
   # run jupyter notebook inside jupyter 
   jupyter-notebook:
-    image:  bfrizzell/mushroom_classifier:a5070bf
+    image:  bfrizzell/mushroom_classifier:f1d0d77
     ports:
       - "8888:8888"
     volumes:

environment.yml

@@ -9,4 +9,7 @@ dependencies:
   - scipy=1.14.1
   - python=3.11
   - pandera=0.21.0
-  - deepchecks=0.3.2
+  - deepchecks=0.3.2
+  - quarto=1.5.57
+  - click=8.1.7
+  - tabulate=0.9.0