From 4c2677774691b51bf7fc9d59e9218eb42f27ad58 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 10:01:59 +0100
Subject: [PATCH 01/20] Add a starting Dockerfile

---
 Dockerfile                    | 60 +++++++++++++++++++++++++++++++++++
 docker/activate-custom-env.sh |  2 ++
 docker/post-build.sh          |  5 +++
 docker/setup_custom_env.py    | 52 ++++++++++++++++++++++++++++++
 4 files changed, 119 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 docker/activate-custom-env.sh
 create mode 100755 docker/post-build.sh
 create mode 100644 docker/setup_custom_env.py

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..ed71d5e5
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,60 @@
+# Use the jupyter/minimal-notebook as the base image
+FROM quay.io/jupyter/minimal-notebook:latest
+
+# Switch to root user to install additional dependencies (if needed)
+USER root
+
+# Install additional dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    build-essential \
+    gcc \
+    g++ \
+    libffi-dev \
+    && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Copy the script to setup the environment
+COPY docker/setup_custom_env.py /opt/setup-scripts/
+# Make the script executable
+RUN chmod +x /opt/setup-scripts/setup_custom_env.py
+
+# Copy the script to activate the Conda environment
+COPY docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
+
+# Switch back to the default notebook user
+USER ${NB_UID}
+
+# Set a shortcut to the tutorial name
+ENV BASENAME="python-tutorial"
+
+# Set the working directory to the home directory of the notebook user
+WORKDIR ${HOME}
+
+# Clone the tutorial repository
+RUN git clone \
+    --branch main \
+    --depth 1 \
+    https://github.com/empa-scientific-it/${BASENAME}
+
+WORKDIR ${HOME}/${BASENAME}
+
+# Create the Conda environment defined in environment.yml
+RUN mamba env create -f binder/environment.yml && \
+    mamba clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# Register the Jupyter kernel from the custom environment
+RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
+
+# Copy the IPython configuration file
+RUN mkdir -p ${HOME}/.ipython/profile_default
+COPY binder/ipython_config.py ${HOME}/.ipython/profile_default/
+
+# Set the environment variable IPYTHONDIR
+ENV IPYTHONDIR="${HOME}/.ipython"
+
+# Use the default ENTRYPOINT from the base image to start Jupyter Lab
+ENTRYPOINT ["tini", "-g", "--", "start.sh"]
diff --git a/docker/activate-custom-env.sh b/docker/activate-custom-env.sh
new file mode 100644
index 00000000..deb43178
--- /dev/null
+++ b/docker/activate-custom-env.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+conda activate python-tutorial
diff --git a/docker/post-build.sh b/docker/post-build.sh
new file mode 100755
index 00000000..90c25f1c
--- /dev/null
+++ b/docker/post-build.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+set -e
+
+mkdir -p ${HOME}/.ipython/profile_default
+cp binder/ipython_config.py ${HOME}/.ipython/profile_default/
diff --git a/docker/setup_custom_env.py b/docker/setup_custom_env.py
new file mode 100644
index 00000000..afcd8e94
--- /dev/null
+++ b/docker/setup_custom_env.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python3
+import json
+import os
+import sys
+from pathlib import Path
+
+# Retrieve the environment name from the command-line arguments
+env_name = sys.argv[1]
+
+# Get the Conda directory from the environment variables
+CONDA_DIR = os.environ["CONDA_DIR"]
+
+# Define the path to the kernel.json file
+kernel_dir = Path.home() / f".local/share/jupyter/kernels/{env_name}"
+kernel_file = kernel_dir / "kernel.json"
+
+# Ensure the kernel directory exists
+kernel_dir.mkdir(parents=True, exist_ok=True)
+
+# Define default kernel.json content
+default_content = {
+    "argv": [
+        f"{CONDA_DIR}/envs/{env_name}/bin/python",
+        "-m",
+        "ipykernel_launcher",
+        "-f",
+        "{connection_file}",
+    ],
+    "display_name": f"Python ({env_name})",
+    "language": "python",
+}
+
+# If the kernel.json file doesn't exist, create it with default content
+if not kernel_file.exists():
+    kernel_file.write_text(json.dumps(default_content, indent=1))
+
+# Read the existing kernel.json content
+content = json.loads(kernel_file.read_text())
+
+# Add the environment variables to the kernel configuration
+content["env"] = {
+    "XML_CATALOG_FILES": "",
+    "PATH": f"{CONDA_DIR}/envs/{env_name}/bin:$PATH",
+    "CONDA_PREFIX": f"{CONDA_DIR}/envs/{env_name}",
+    "CONDA_PROMPT_MODIFIER": f"({env_name}) ",
+    "CONDA_SHLVL": "2",
+    "CONDA_DEFAULT_ENV": env_name,
+    "CONDA_PREFIX_1": CONDA_DIR,
+}
+
+# Write the updated content back to the kernel.json file
+kernel_file.write_text(json.dumps(content, indent=1))

From 3ac0f441c9d8ac355b3aba2ffae5527bca87c586 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 13:20:49 +0100
Subject: [PATCH 02/20] Paths fixed

---
 Dockerfile | 40 ++++++++++++++++++++++------------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ed71d5e5..70984b9a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,22 @@
 # Use the jupyter/minimal-notebook as the base image
 FROM quay.io/jupyter/minimal-notebook:latest
 
+# Set a shortcut to the tutorial name
+ENV BASENAME="python-tutorial"
+ENV REPO="https://github.com/edoardob90/${BASENAME}"
+
+# Set the working directory to the home directory of the notebook user
+WORKDIR ${HOME}
+
+# Clone the tutorial repository
+RUN git clone \
+    --branch add-dockerfile \
+    --depth 1 \
+    ${REPO}
+
+# Set the working directory to the repository directory
+WORKDIR ${BASENAME}
+
 # Switch to root user to install additional dependencies (if needed)
 USER root
 
@@ -16,29 +32,17 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/*
 
 # Copy the script to setup the environment
-COPY docker/setup_custom_env.py /opt/setup-scripts/
-# Make the script executable
-RUN chmod +x /opt/setup-scripts/setup_custom_env.py
+RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
+    chmod +x /opt/setup-scripts/setup_custom_env.py
 
 # Copy the script to activate the Conda environment
-COPY docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
+RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
 
 # Switch back to the default notebook user
 USER ${NB_UID}
 
-# Set a shortcut to the tutorial name
-ENV BASENAME="python-tutorial"
-
-# Set the working directory to the home directory of the notebook user
-WORKDIR ${HOME}
-
-# Clone the tutorial repository
-RUN git clone \
-    --branch main \
-    --depth 1 \
-    https://github.com/empa-scientific-it/${BASENAME}
-
-WORKDIR ${HOME}/${BASENAME}
+# Set the working directory to the repository directory
+# WORKDIR ${HOME}/${BASENAME}
 
 # Create the Conda environment defined in environment.yml
 RUN mamba env create -f binder/environment.yml && \
@@ -49,7 +53,7 @@ RUN mamba env create -f binder/environment.yml && \
 # Register the Jupyter kernel from the custom environment
 RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
 
-# Copy the IPython configuration file
+# Copy the IPython configuration file (binder/postBuild script)
 RUN mkdir -p ${HOME}/.ipython/profile_default
 COPY binder/ipython_config.py ${HOME}/.ipython/profile_default/
 

From dd70a0e41a1c683a387b487093d05b5844f55fe6 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 14:05:51 +0100
Subject: [PATCH 03/20] Use base environment

---
 Dockerfile             | 17 +++++++----------
 docker/environment.yml | 23 +++++++++++++++++++++++
 2 files changed, 30 insertions(+), 10 deletions(-)
 create mode 100644 docker/environment.yml

diff --git a/Dockerfile b/Dockerfile
index 70984b9a..76bf767f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -32,30 +32,27 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/*
 
 # Copy the script to setup the environment
-RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
-    chmod +x /opt/setup-scripts/setup_custom_env.py
+# RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
+#     chmod +x /opt/setup-scripts/setup_custom_env.py
 
 # Copy the script to activate the Conda environment
-RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
+# RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
 
 # Switch back to the default notebook user
 USER ${NB_UID}
 
-# Set the working directory to the repository directory
-# WORKDIR ${HOME}/${BASENAME}
-
 # Create the Conda environment defined in environment.yml
-RUN mamba env create -f binder/environment.yml && \
+RUN mamba env update -f docker/environment.yml && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
 # Register the Jupyter kernel from the custom environment
-RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
+# RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
 
 # Copy the IPython configuration file (binder/postBuild script)
-RUN mkdir -p ${HOME}/.ipython/profile_default
-COPY binder/ipython_config.py ${HOME}/.ipython/profile_default/
+RUN mkdir -p ${HOME}/.ipython/profile_default && \
+    cp -a binder/ipython_config.py ${HOME}/.ipython/profile_default/
 
 # Set the environment variable IPYTHONDIR
 ENV IPYTHONDIR="${HOME}/.ipython"
diff --git a/docker/environment.yml b/docker/environment.yml
new file mode 100644
index 00000000..ade81543
--- /dev/null
+++ b/docker/environment.yml
@@ -0,0 +1,23 @@
+---
+name: base
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - pip:
+      - numpy
+      - matplotlib
+      - pandas
+      - ipywidgets
+      - ipynbname
+      - jupyterlab
+      - pytest
+      - pytest-timeout
+      - markdown
+      - pre-commit
+      - geostatspy
+      - gstools
+      - scikit-learn
+      - attrs
+      - multiprocess

From a1ef367c337a58cbb0eb7b2857c480677fdd4f61 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 14:37:48 +0100
Subject: [PATCH 04/20] Remove pinned python version

---
 Dockerfile             | 15 +++------------
 docker/environment.yml |  1 -
 2 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 76bf767f..6b1903e6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,7 +10,7 @@ WORKDIR ${HOME}
 
 # Clone the tutorial repository
 RUN git clone \
-    --branch add-dockerfile \
+    --branch main \
     --depth 1 \
     ${REPO}
 
@@ -31,25 +31,16 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-# Copy the script to setup the environment
-# RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
-#     chmod +x /opt/setup-scripts/setup_custom_env.py
-
-# Copy the script to activate the Conda environment
-# RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
-
 # Switch back to the default notebook user
 USER ${NB_UID}
 
 # Create the Conda environment defined in environment.yml
-RUN mamba env update -f docker/environment.yml && \
+# COPY --chown=${NB_USER}:${NB_GID} docker/environment.yml docker/environment.yml
+RUN mamba env update -n base -f docker/environment.yml && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Register the Jupyter kernel from the custom environment
-# RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
-
 # Copy the IPython configuration file (binder/postBuild script)
 RUN mkdir -p ${HOME}/.ipython/profile_default && \
     cp -a binder/ipython_config.py ${HOME}/.ipython/profile_default/
diff --git a/docker/environment.yml b/docker/environment.yml
index ade81543..5e4420c7 100644
--- a/docker/environment.yml
+++ b/docker/environment.yml
@@ -3,7 +3,6 @@ name: base
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
   - pip
   - pip:
       - numpy

From 46fd36f324302a88f565ed7266c9b953e04d6567 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 15:16:15 +0100
Subject: [PATCH 05/20] Optimize Docker image build

---
 .dockerignore |  4 ++++
 Dockerfile    | 44 +++++++++++++++++---------------------------
 2 files changed, 21 insertions(+), 27 deletions(-)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..8513c1d3
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,4 @@
+.git
+slides/
+.DS_Store
+__pycache__/
diff --git a/Dockerfile b/Dockerfile
index 6b1903e6..2d980eb4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,52 +1,42 @@
 # Use the jupyter/minimal-notebook as the base image
 FROM quay.io/jupyter/minimal-notebook:latest
 
-# Set a shortcut to the tutorial name
+# Set environment variables for the tutorial and repository
 ENV BASENAME="python-tutorial"
-ENV REPO="https://github.com/edoardob90/${BASENAME}"
-
-# Set the working directory to the home directory of the notebook user
-WORKDIR ${HOME}
-
-# Clone the tutorial repository
-RUN git clone \
-    --branch main \
-    --depth 1 \
-    ${REPO}
-
-# Set the working directory to the repository directory
-WORKDIR ${BASENAME}
+ENV REPO=${HOME}/${BASENAME}
+ENV IPYTHONDIR="${HOME}/.ipython"
 
-# Switch to root user to install additional dependencies (if needed)
+# Switch to root user to install additional dependencies
 USER root
-
-# Install additional dependencies
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     build-essential \
     gcc \
     g++ \
-    libffi-dev \
-    && \
+    libffi-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 # Switch back to the default notebook user
 USER ${NB_UID}
 
-# Create the Conda environment defined in environment.yml
-# COPY --chown=${NB_USER}:${NB_GID} docker/environment.yml docker/environment.yml
-RUN mamba env update -n base -f docker/environment.yml && \
+# Set up the Conda environment
+COPY docker/environment.yml /tmp/environment.yml
+RUN mamba env update -n base -f /tmp/environment.yml && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Copy the IPython configuration file (binder/postBuild script)
-RUN mkdir -p ${HOME}/.ipython/profile_default && \
-    cp -a binder/ipython_config.py ${HOME}/.ipython/profile_default/
+# Prepare IPython configuration (move earlier in the build)
+RUN mkdir -p ${HOME}/.ipython/profile_default
+COPY --chown=${NB_UID}:${NB_GID} binder/ipython_config.py ${HOME}/.ipython/profile_default/
 
-# Set the environment variable IPYTHONDIR
-ENV IPYTHONDIR="${HOME}/.ipython"
+# Copy the repository late in the build process
+RUN mkdir -p ${REPO}
+COPY --chown=${NB_UID}:${NB_GID} . ${REPO}/
+
+# Set the working directory to the repository
+WORKDIR ${REPO}
 
 # Use the default ENTRYPOINT from the base image to start Jupyter Lab
 ENTRYPOINT ["tini", "-g", "--", "start.sh"]

From ebab11842bf35f011e0be3ec07699bb01ac6e394 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 15:29:51 +0100
Subject: [PATCH 06/20] Add metadata labels

---
 Dockerfile | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 2d980eb4..7fdae0f6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,15 @@
 # Use the jupyter/minimal-notebook as the base image
 FROM quay.io/jupyter/minimal-notebook:latest
 
+# Metadata labels
+LABEL org.opencontainers.image.title="Python Tutorial"
+LABEL org.opencontainers.image.description="A containerized Python tutorial environment with Jupyter Lab."
+LABEL org.opencontainers.image.authors="Empa Scientific IT <scientificit@empa.ch>"
+LABEL org.opencontainers.image.url="https://github.com/empa-scientific-it/python-tutorial"
+LABEL org.opencontainers.image.source="https://github.com/empa-scientific-it/python-tutorial"
+LABEL org.opencontainers.image.version="1.0.0"
+LABEL org.opencontainers.image.licenses="MIT"
+
 # Set environment variables for the tutorial and repository
 ENV BASENAME="python-tutorial"
 ENV REPO=${HOME}/${BASENAME}

From 7a939de1284f49fc1706c128addab31f1dc245b8 Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Wed, 20 Nov 2024 15:30:44 +0100
Subject: [PATCH 07/20] Add GitHub workflow

---
 .github/workflows/docker-build.yml            | 36 +++++++++++++++++++
 ...build-docker-image.yml => repo2docker.yml} |  0
 2 files changed, 36 insertions(+)
 create mode 100644 .github/workflows/docker-build.yml
 rename .github/workflows/{build-docker-image.yml => repo2docker.yml} (100%)

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
new file mode 100644
index 00000000..3191db75
--- /dev/null
+++ b/.github/workflows/docker-build.yml
@@ -0,0 +1,36 @@
+name: Build Tutorial Container
+
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "*.md"
+      - slides/**
+      - images/**
+      - .gitignore
+  workflow_dispatch:
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build the Docker image
+        run: |
+          docker build -t ghcr.io/${{ github.repository }}:latest .
+
+      - name: Push the Docker image
+        run: |
+          docker push ghcr.io/${{ github.repository }}:latest
diff --git a/.github/workflows/build-docker-image.yml b/.github/workflows/repo2docker.yml
similarity index 100%
rename from .github/workflows/build-docker-image.yml
rename to .github/workflows/repo2docker.yml

From fe3520f23d5fc539bba775cedf3229295f25f3c3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 20 Nov 2024 14:38:40 +0000
Subject: [PATCH 08/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/workflows/docker-build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 3191db75..d986d7d4 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -1,3 +1,4 @@
+---
 name: Build Tutorial Container
 
 on:

From 521ae7b4f5bbb841593d6844a1c62b9de29b4cdc Mon Sep 17 00:00:00 2001
From: edoardob90 <edoardob90@gmail.com>
Date: Fri, 22 Nov 2024 11:21:13 +0100
Subject: [PATCH 09/20] Add AI dependencies

---
 binder/environment.yml | 4 ++++
 docker/environment.yml | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/binder/environment.yml b/binder/environment.yml
index 7d382e1d..60d0322a 100644
--- a/binder/environment.yml
+++ b/binder/environment.yml
@@ -21,3 +21,7 @@ dependencies:
       - scikit-learn
       - attrs
       - multiprocess
+      - openai
+      - tenacity
+      - markdown2
+      - python-dotenv
diff --git a/docker/environment.yml b/docker/environment.yml
index 5e4420c7..b9a588de 100644
--- a/docker/environment.yml
+++ b/docker/environment.yml
@@ -20,3 +20,7 @@ dependencies:
       - scikit-learn
       - attrs
       - multiprocess
+      - openai
+      - tenacity
+      - markdown2
+      - python-dotenv

From 6d1f3811d967981f34a929af3e78c29a24540cc7 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 25 Nov 2024 21:33:37 +0100
Subject: [PATCH 10/20] Remove unused files

---
 docker/activate-custom-env.sh |  2 --
 docker/post-build.sh          |  5 ----
 docker/setup_custom_env.py    | 52 -----------------------------------
 3 files changed, 59 deletions(-)
 delete mode 100644 docker/activate-custom-env.sh
 delete mode 100755 docker/post-build.sh
 delete mode 100644 docker/setup_custom_env.py

diff --git a/docker/activate-custom-env.sh b/docker/activate-custom-env.sh
deleted file mode 100644
index deb43178..00000000
--- a/docker/activate-custom-env.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-conda activate python-tutorial
diff --git a/docker/post-build.sh b/docker/post-build.sh
deleted file mode 100755
index 90c25f1c..00000000
--- a/docker/post-build.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-set -e
-
-mkdir -p ${HOME}/.ipython/profile_default
-cp binder/ipython_config.py ${HOME}/.ipython/profile_default/
diff --git a/docker/setup_custom_env.py b/docker/setup_custom_env.py
deleted file mode 100644
index afcd8e94..00000000
--- a/docker/setup_custom_env.py
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env python3
-import json
-import os
-import sys
-from pathlib import Path
-
-# Retrieve the environment name from the command-line arguments
-env_name = sys.argv[1]
-
-# Get the Conda directory from the environment variables
-CONDA_DIR = os.environ["CONDA_DIR"]
-
-# Define the path to the kernel.json file
-kernel_dir = Path.home() / f".local/share/jupyter/kernels/{env_name}"
-kernel_file = kernel_dir / "kernel.json"
-
-# Ensure the kernel directory exists
-kernel_dir.mkdir(parents=True, exist_ok=True)
-
-# Define default kernel.json content
-default_content = {
-    "argv": [
-        f"{CONDA_DIR}/envs/{env_name}/bin/python",
-        "-m",
-        "ipykernel_launcher",
-        "-f",
-        "{connection_file}",
-    ],
-    "display_name": f"Python ({env_name})",
-    "language": "python",
-}
-
-# If the kernel.json file doesn't exist, create it with default content
-if not kernel_file.exists():
-    kernel_file.write_text(json.dumps(default_content, indent=1))
-
-# Read the existing kernel.json content
-content = json.loads(kernel_file.read_text())
-
-# Add the environment variables to the kernel configuration
-content["env"] = {
-    "XML_CATALOG_FILES": "",
-    "PATH": f"{CONDA_DIR}/envs/{env_name}/bin:$PATH",
-    "CONDA_PREFIX": f"{CONDA_DIR}/envs/{env_name}",
-    "CONDA_PROMPT_MODIFIER": f"({env_name}) ",
-    "CONDA_SHLVL": "2",
-    "CONDA_DEFAULT_ENV": env_name,
-    "CONDA_PREFIX_1": CONDA_DIR,
-}
-
-# Write the updated content back to the kernel.json file
-kernel_file.write_text(json.dumps(content, indent=1))

From 3786be671ca9de635d799102d3055f7417dac19a Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 25 Nov 2024 21:45:18 +0100
Subject: [PATCH 11/20] Use official actions

---
 .github/workflows/docker-build.yml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index d986d7d4..ef1de6d2 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -18,8 +18,8 @@ jobs:
     permissions:
       packages: write
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
+      - name: Setup Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to GHCR
         uses: docker/login-action@v3
@@ -28,10 +28,9 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build the Docker image
-        run: |
-          docker build -t ghcr.io/${{ github.repository }}:latest .
-
-      - name: Push the Docker image
-        run: |
-          docker push ghcr.io/${{ github.repository }}:latest
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: ghcr.io/${{ github.repository }}:latest

From ee4f830d1d3776cf1bdcd3ba57d848990e9bb328 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Sun, 4 May 2025 21:43:17 +0200
Subject: [PATCH 12/20] Update environment.yml

---
 docker/environment.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docker/environment.yml b/docker/environment.yml
index b9a588de..6df2975c 100644
--- a/docker/environment.yml
+++ b/docker/environment.yml
@@ -24,3 +24,10 @@ dependencies:
       - tenacity
       - markdown2
       - python-dotenv
+      - pillow
+      - opencv-python
+      - torch
+      - torchaudio
+      - torchvision
+      - albumentations
+      - grad-cam

From 1fbd74e28fdeb15f7afaea804e39defe0c506b0b Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 10:53:07 +0200
Subject: [PATCH 13/20] Remove COPY command

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7fdae0f6..2b61e3f6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -41,8 +41,8 @@ RUN mkdir -p ${HOME}/.ipython/profile_default
 COPY --chown=${NB_UID}:${NB_GID} binder/ipython_config.py ${HOME}/.ipython/profile_default/
 
 # Copy the repository late in the build process
-RUN mkdir -p ${REPO}
-COPY --chown=${NB_UID}:${NB_GID} . ${REPO}/
+# RUN mkdir -p ${REPO}
+# COPY --chown=${NB_UID}:${NB_GID} . ${REPO}/
 
 # Set the working directory to the repository
 WORKDIR ${REPO}

From 6b7023eb4e2e6a14d372fef2d78c1d5daf15a71b Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 11:31:23 +0200
Subject: [PATCH 14/20] Rename workflow

---
 .github/workflows/repo2docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml
index 035cb9a9..f3eb9450 100644
--- a/.github/workflows/repo2docker.yml
+++ b/.github/workflows/repo2docker.yml
@@ -1,5 +1,5 @@
 ---
-name: Build Tutorial Container
+name: Build Container with repo2docker
 on:
   push:
     branches:

From fc29c4d961a6eb17fd603b5e29adcc60cf0eed18 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 11:31:35 +0200
Subject: [PATCH 15/20] Add missing dependency

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 2b61e3f6..ec85241c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,7 +22,8 @@ RUN apt-get update && \
     build-essential \
     gcc \
     g++ \
-    libffi-dev && \
+    libffi-dev \
+    libgl1 && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 

From b73f19fe3a73fcbc1db911269e237b766556d410 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 11:45:41 +0200
Subject: [PATCH 16/20] Update instructions to run Docker

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b09bbdce..b7bb9520 100644
--- a/README.md
+++ b/README.md
@@ -93,7 +93,7 @@ docker pull ghcr.io/empa-scientific-it/python-tutorial:latest
 5. Run the Docker container: Once the image is downloaded, run the following command to start a Docker container from the image:
 
 ```console
-docker run -p  8888:8888  --name python_tutorial -v /path/to/python-tutorial:/home/jovyan/work ghcr.io/empa-scientific-it/python-tutorial:latest jupyter lab --ip 0.0.0.0 --no-browser
+docker run -p 8888:8888 --name python_tutorial -v /path/to/python-tutorial:/home/jovyan/python-tutorial ghcr.io/empa-scientific-it/python-tutorial:latest jupyter lab --ip 0.0.0.0 --no-browser
 ```
 
 Replace `/path/to/python-tutorial` with the path to the folder you created in step 2, for example `C:/Users/yourusername/Desktop/python-tutorial`.

From 21ffc79291073089a2099896c20df5db05c031a8 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 15:25:17 +0200
Subject: [PATCH 17/20] Remove old workflow

---
 .github/workflows/repo2docker.yml | 28 ----------------------------
 1 file changed, 28 deletions(-)
 delete mode 100644 .github/workflows/repo2docker.yml

diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml
deleted file mode 100644
index f3eb9450..00000000
--- a/.github/workflows/repo2docker.yml
+++ /dev/null
@@ -1,28 +0,0 @@
----
-name: Build Container with repo2docker
-on:
-  push:
-    branches:
-      - main
-    paths-ignore:
-      - "*.md"
-      - slides/**
-      - images/**
-      - .gitignore
-  workflow_dispatch:
-jobs:
-  repo2docker:
-    runs-on: ubuntu-latest
-    permissions:
-      packages: write
-    steps:
-      - name: checkout files in repo
-        uses: actions/checkout@main
-      - name: update jupyter dependencies with repo2docker
-        uses: jupyterhub/repo2docker-action@master
-        with:
-          DOCKER_USERNAME: ${{ github.actor }}
-          DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
-          DOCKER_REGISTRY: ghcr.io
-          IMAGE_NAME: ${{ github.repository }}
-          FORCE_REPO2DOCKER_VERSION: jupyter-repo2docker==2024.07.0

From 0aad7809058f98aadf170375bebe73f1654a7d91 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 15:27:27 +0200
Subject: [PATCH 18/20] Adjust workflow

* Trigger build for PR, but only when from the same repo
* Multi-arch build
* Uses "docker/metadata" action to set up labels and tags
---
 .github/workflows/docker-build.yml | 38 +++++++++++++++++++++++++++---
 1 file changed, 35 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index ef1de6d2..61e51fb8 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -10,6 +10,12 @@ on:
       - slides/**
       - images/**
       - .gitignore
+  pull_request:
+    paths-ignore:
+      - "*.md"
+      - slides/**
+      - images/**
+      - .gitignore
   workflow_dispatch:
 
 jobs:
@@ -17,20 +23,46 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       packages: write
+    strategy:
+      matrix:
+        arch: [amd64, arm64]
+      fail-fast: false
     steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       - name: Setup Docker Buildx
         uses: docker/setup-buildx-action@v3
 
       - name: Log in to GHCR
+        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
         uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.arch == 'amd64' }}
+            type=ref,event=branch
+            type=ref,event=pr
+            type=sha,format=short
+          flavor: |
+            suffix=-${{ matrix.arch }}
+
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
-          platforms: linux/amd64,linux/arm64
-          push: true
-          tags: ghcr.io/${{ github.repository }}:latest
+          context: .
+          platforms: linux/${{ matrix.arch }}
+          push: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

From edcb8aae159943862143cf8cf76288f53dbd5989 Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 15:47:12 +0200
Subject: [PATCH 19/20] Remove COPY

---
 Dockerfile | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ec85241c..cf496d34 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -41,10 +41,6 @@ RUN mamba env update -n base -f /tmp/environment.yml && \
 RUN mkdir -p ${HOME}/.ipython/profile_default
 COPY --chown=${NB_UID}:${NB_GID} binder/ipython_config.py ${HOME}/.ipython/profile_default/
 
-# Copy the repository late in the build process
-# RUN mkdir -p ${REPO}
-# COPY --chown=${NB_UID}:${NB_GID} . ${REPO}/
-
 # Set the working directory to the repository
 WORKDIR ${REPO}
 

From 5df484c7dd425b53b6b8ad4f7240ef590a4f0f0d Mon Sep 17 00:00:00 2001
From: Edoardo Baldi <edoardob90@gmail.com>
Date: Mon, 5 May 2025 15:56:09 +0200
Subject: [PATCH 20/20] Update Docker tags

* Keep only branch, pr, and SHA
* Add repo tags vX.Y or vX.Y.Z
---
 .github/workflows/docker-build.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 61e51fb8..5762f13b 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -10,6 +10,9 @@ on:
       - slides/**
       - images/**
       - .gitignore
+    tags:
+      - "v*.*"
+      - "v*.*.*"
   pull_request:
     paths-ignore:
       - "*.md"
@@ -51,12 +54,10 @@ jobs:
         with:
           images: ghcr.io/${{ github.repository }}
           tags: |
-            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.arch == 'amd64' }}
-            type=ref,event=branch
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}
             type=ref,event=pr
+            type=ref,event=tag
             type=sha,format=short
-          flavor: |
-            suffix=-${{ matrix.arch }}
 
       - name: Build and push
         uses: docker/build-push-action@v6