Merge pull request #349 from pyiron/rebuild

Fix conda update bug - always include all requirements by merging the environment files
pyiron · Aug 1, 2024 · df29c59 · df29c59
2 parents b341995 + 4d14948
commit df29c59
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Showing 8 changed files with 102 additions and 61 deletions.
diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Get current date
         id: date
         run: echo "date=$(date +%F)" >> $GITHUB_OUTPUT
@@ -20,20 +20,40 @@ jobs:
           message: ""
       - name: Login to DockerHub Registry
         run: echo ${{ secrets.DOCKERHUB_PASSWORD }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
-      - run: docker build -t pyiron/base:latest base/
-      - run: docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
-      - run: docker build -t pyiron/md:latest md/
-      - run: docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
-      - run: docker build -t pyiron/pyiron:latest pyiron/
-      - run: docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
-      - run: docker build -t pyiron/potentialworkshop:latest potentialworkshop/
-      - run: docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
-      - run: docker build -t pyiron/experimental:latest experimental/
-      - run: docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
-      - run: docker build -t pyiron/continuum:latest continuum/
-      - run: docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
-      - run: docker build -t pyiron/mpie_cmti:latest mpie_cmti/
-      - run: docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
+      - name: Build pyiron/base
+        run: |
+          docker build -t pyiron/base:latest base/
+          docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
+      - name: Build pyiron/md
+        run: |
+          tail --lines=+4 base/environment.yml >> md/environment.yml
+          docker build -t pyiron/md:latest md/
+          docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
+      - name: Build pyiron/continuum
+        run: |
+          docker build -t pyiron/continuum:latest continuum/
+          docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
+      - name: Build pyiron/pyiron
+        run: |
+          tail --lines=+4 md/environment.yml >> pyiron/environment.yml
+          docker build -t pyiron/pyiron:latest pyiron/
+          docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
+      - name: Build pyiron/potentialworkshop
+        run: | 
+          tail --lines=+4 pyiron/environment.yml >> potentialworkshop/environment.yml
+          docker build -t pyiron/potentialworkshop:latest potentialworkshop/
+          docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
+      - name: Build pyiron/experimental
+        run: |
+          tail --lines=+4 base/environment.yml >> experimental/environment.yml
+          docker build -t pyiron/experimental:latest experimental/
+          docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
+      - name: Build pyiron/mpie_cmti
+        run: |
+          tail --lines=+4 pyiron/environment.yml >> mpie_cmti/environment.yml
+          docker build -t pyiron/mpie_cmti:latest mpie_cmti/
+          docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
+      # Publish
       - run: docker images
       - run: docker push pyiron/base:latest
       - run: docker push pyiron/base:"$(date +%F)"
@@ -49,6 +69,7 @@ jobs:
       - run: docker push pyiron/continuum:"$(date +%F)"
       - run: docker push pyiron/mpie_cmti:latest
       - run: docker push pyiron/mpie_cmti:"$(date +%F)"
+      # Export Environments
       - run: mkdir -p environment; chmod 777 environment
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_base_$(date +%F).yml;' 
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/md /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_md_$(date +%F).yml;' 

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -8,26 +8,47 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - run: docker build -t pyiron/base:latest base/
-      - run: docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
-      - run: docker build -t pyiron/md:latest md/
-      - run: docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
-      - run: docker build -t pyiron/continuum:latest continuum/
-      - run: docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
-      - run: docker build -t pyiron/pyiron:latest pyiron/
-      - run: docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
-      - run: docker build -t pyiron/potentialworkshop:latest potentialworkshop/
-      - run: docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
-      - run: docker build -t pyiron/experimental:latest experimental/
-      - run: docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
-      - run: docker build -t pyiron/mpie_cmti:latest mpie_cmti/
-      - run: docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
+      - uses: actions/checkout@v4
+      - name: Build pyiron/base
+        run: |
+          docker build -t pyiron/base:latest base/
+          docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
+      - name: Build pyiron/md
+        run: |
+          tail --lines=+4 base/environment.yml >> md/environment.yml
+          docker build -t pyiron/md:latest md/
+          docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
+      - name: Build pyiron/continuum
+        run: |
+          docker build -t pyiron/continuum:latest continuum/
+          docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
+      - name: Build pyiron/pyiron
+        run: |
+          tail --lines=+4 md/environment.yml >> pyiron/environment.yml
+          docker build -t pyiron/pyiron:latest pyiron/
+          docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
+      - name: Build pyiron/potentialworkshop
+        run: | 
+          tail --lines=+4 pyiron/environment.yml >> potentialworkshop/environment.yml
+          docker build -t pyiron/potentialworkshop:latest potentialworkshop/
+          docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
+      - name: Build pyiron/experimental
+        run: |
+          tail --lines=+4 base/environment.yml >> experimental/environment.yml
+          docker build -t pyiron/experimental:latest experimental/
+          docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
+      - name: Build pyiron/mpie_cmti
+        run: |
+          tail --lines=+4 pyiron/environment.yml >> mpie_cmti/environment.yml
+          docker build -t pyiron/mpie_cmti:latest mpie_cmti/
+          docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
+      # Testing
       - run: docker images
       - run: docker run --rm pyiron/continuum /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
       - run: docker run --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'  
       - run: docker run --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
       - run: docker run --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
+      # Export Environments
       - run: mkdir -p environment; chmod 777 environment
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_base_$(date +%F).yml;' 
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/md /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_md_$(date +%F).yml;' 

diff --git a/base/environment.yml b/base/environment.yml
@@ -2,6 +2,4 @@ channels:
 - conda-forge
 dependencies:
 - pyiron_base =0.9.10
-- git =2.42.0
-- openmpi =4.1.6
-- hdf5 =1.14.3=mpi_openmpi_*
+- git =2.46.0
diff --git a/continuum/environment.yml b/continuum/environment.yml
@@ -4,11 +4,18 @@ dependencies:
 - damask =3.0.0a8
 - fenics =2019.1.0=*_42
 - mshr =2019.1.0=*_9
+- pyiron =0.5.2
 - pyiron_base =0.8.2
 - pyiron_atomistics =0.5.3
 - pyiron_continuum =0.0.8
 - pyiron_gpl =0.0.5
+- pyiron-data =0.0.30
 - pyvista =0.43.6
 - sqsgenerator =0.3
 - vtk =9.2.6
 - seaborn =0.13.2
+- nglview =3.1.2
+- lammps =2024.02.07=*openmpi*
+- openkim-models =2021.01.28
+- git =2.42.0
+- openmpi =4.1.6
diff --git a/md/environment.yml b/md/environment.yml
@@ -3,7 +3,7 @@ channels:
 dependencies:
 - pyiron =0.5.2
 - pyiron_atomistics =0.6.9
-- pyiron-data =0.0.29
+- pyiron-data =0.0.30
 - nglview =3.1.2
-- lammps =2023.11.21=*openmpi*
+- lammps =2023.08.02=*openmpi*
 - openkim-models =2021.01.28
diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml
@@ -1,30 +1,26 @@
 channels:
 - conda-forge
 dependencies:
-- atomicrex =1.0.3
-- calphy =1.3.8
-- fitsnap3 =3.1.0.1
+- atomicrex =1.0.4
+- calphy =1.3.10
+- fitsnap3 =3.1.0.4
 - nbgitpuller =1.2.1
-- pyiron_base =0.9.10
-- pyiron_atomistics =0.6.9
-- pyiron_snippets =0.1.3
-- pyiron_contrib =0.1.16
-- pyiron_potentialfit =0.3.2
+- pyiron_contrib =0.1.17
+- pyiron_potentialfit =0.3.4
 - pyiron_workflow =0.9.4
 - pyiron_gui =0.0.12
-- matgl =0.9.2
+- matgl =1.1.2
 - mlip =2.0
 - sqsgenerator =0.3
 - pyiron_gpl =0.0.5
 - python-ace =0.3.0
-- pytorch =2.0.0
+- pytorch =2.1.2
 - pyxtal =0.6.7
-- runner =1.2
+- runner =1.3
 - structdbrest =0.0.1
-- tensorflow =2.15.0
+- tensorflow =2.16.2
 - psycopg2 =2.9.9
-- netCDF4 =1.6.5
-- numba =0.59.0
-- llama-index =0.10.33
-- jupyter-server-proxy =4.1.2
+- numba =0.60.0
+- llama-index =0.10.59
+- jupyter-server-proxy =4.3.0
 - flux-core =0.64.0
diff --git a/potentialworkshop/environment.yml b/potentialworkshop/environment.yml
@@ -8,5 +8,5 @@ dependencies:
 - pyiron_gpl =0.0.5
 - nbgitpuller =1.2.1
 - python-ace =0.3.0
-- calphy =1.3.7
+- calphy =1.3.10
 - pyxtal =0.6.7
diff --git a/requirements.txt b/requirements.txt
@@ -2,18 +2,17 @@ pyiron==0.5.2
 pyiron_base==0.9.10
 pyiron-atomistics==0.6.9
 pyiron-continuum==0.0.8
-pyiron-contrib==0.1.16
+pyiron-contrib==0.1.17
 pyiron_experimental==0.0.3
 pyiron_workflow==0.9.4
 pyiron-gpl==0.0.5
-pyiron_snippets==0.1.1
-pyiron_potentialfit==0.3.2
-calphy==1.3.8
+pyiron_potentialfit==0.3.4
+calphy==1.3.10
 damask==3.0.0a8
 fenics==2019.1.0
 gpaw==24.6.0
 hyperspy==2.1.1
-jupyter-server-proxy==4.1.2
+jupyter-server-proxy==4.3.0
 nbgitpuller==1.2.1
 nglview==3.1.2
 pystem==0.0.26
@@ -23,10 +22,9 @@ pyxem==0.19.1
 pyxtal==0.6.7
 scanf==1.5.2
 seaborn==0.13.2
-sqlalchemy==2.0.30
 structdbrest==0.0.1
 temmeta==0.0.6
 vtk==9.2.6
-pytorch==2.0.0
-tensorflow==2.15.0
-llama-index==0.10.33
+pytorch==2.1.2
+tensorflow==2.16.2
+llama-index==0.10.59