Merge pull request #13 from SchmidtDSE/debug/env

Solved env issues using new mesa-geo and pixi(!) - plus much better logging and some basic veg debug

.devcontainer/.gitattributes

@@ -0,0 +1,3 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.devcontainer/.gitignore

@@ -0,0 +1,3 @@
+# pixi environments
+.pixi
+

.devcontainer/Dockerfile

@@ -1,18 +1,21 @@
-# First, grab a Unix image with Python / Conda installed
-FROM condaforge/miniforge3
+# First, grab a Unix image with pixi installed
+FROM ghcr.io/prefix-dev/pixi:0.18.0
 
 # Copy over install scripts - this is a good way to keep the Dockerfile clean and readable
 COPY .devcontainer/scripts .devcontainer/scripts
 
-# Install git and ssh (note that you could also put this in a .sh for better readability)
+# Install git, ssh
 RUN .devcontainer/scripts/install_git_and_ssh.sh
 
-# Then, copy the .devcontainer contents of the repo into the image - note we do this later so that we can avoid re-installing sys dependencies if the python deps change
-COPY .devcontainer/python_environment.yml .devcontainer/python_environment.yml
-RUN conda env create -f .devcontainer/python_environment.yml
+# Copy over pixi toml and pyproject.toml
+COPY pixi.toml pixi.toml
+COPY pixi.lock pixi.lock
+
+# Install pixi dependencies
+RUN pixi install
 
 # Now, copy python source code into the image - by doing this last, we can avoid re-installing ALL dependencies if just the source code changes
-COPY rainfall rainfall
+COPY vegetation vegetation
 
 # Finally, keep the container running so that we can attach to it
 CMD tail -f /dev/null

.devcontainer/devcontainer.json

@@ -5,7 +5,13 @@
     "context": "../"
   },
   "mounts": [
-    "source=${localEnv:HOME}/.ssh,target=/root/.ssh,type=bind" // SSH keys
+    "source=${localEnv:HOME}/.ssh,target=/root/.ssh,type=bind", // SSH keys
+    "source=/local_dev_data,target=/local_dev_data,type=bind" // Local development cache
   ],
-  "extensions": ["ms-python.flake8", "ms-python.python", "ms-python.debugpy"]
+  "extensions": [
+    "ms-python.flake8",
+    "ms-python.python",
+    "ms-python.debugpy",
+    "ms-python.black-formatter"
+  ]
 }

.devcontainer/scripts/install_pixi.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+curl -fsSL https://pixi.sh/install.sh | bash
+export "eval "$(pixi completion --shell bash)" >> ~/.bashrc

.gitattributes

@@ -0,0 +1,3 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/workflows/todos_to_issues.yml

@@ -0,0 +1,27 @@
+name: "Run TODO to Issue"
+on: ["push"]
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: "actions/checkout@v4"
+      - name: "TODO to Issue"
+        uses: "alstr/todo-to-issue-action@v5"
+        with:
+          INSERT_ISSUE_URLS: "true"
+          CLOSE_ISSUES: "true"
+
+      - name: Set Git user
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Commit and Push Changes
+        run: |
+          git add -A
+          if [[ `git status --porcelain` ]]; then
+            git commit -m "Automatically added GitHub issue links to TODOs"
+            git push
+          else
+            echo "No changes to commit"
+          fi

.gitignore

@@ -1,4 +1,8 @@
 *.csv
 .env
 __pycache__/
-*.pyc
+*.pyc
+tst*.*
+vegetation/profile_output.prof# pixi environments
+.pixi
+

.vscode/launch.json

@@ -5,12 +5,12 @@
       "name": "Solara: Launch",
       "type": "debugpy",
       "request": "launch",
-      "cwd": "${workspaceFolder}/rainfall",
+      "cwd": "${workspaceFolder}/vegetation",
       "module": "solara",
       "args": ["run", "app.py"],
       "console": "integratedTerminal",
       "justMyCode": false,
-      "pythonPath": "/opt/conda/envs/mesa/bin/python"
+      "pythonPath": "/workspaces/mesa_abm_poc/.pixi/envs/default/bin/python"
     }
   ]
 }

pixi.toml

@@ -0,0 +1,37 @@
+[project]
+name = "mesa"
+version = "0.1.0"
+description = "Add a short description here"
+authors = ["GondekNP <[email protected]>"]
+channels = ["main", "r", "msys2", "conda-forge"]
+platforms = ["linux-64"]
+
+[tasks]
+
+[dependencies]
+
+[target.linux-64.dependencies]
+python = "3.11.*"
+debugpy = "*"
+ipython = "*"
+python-dotenv = "*"
+planetary-computer = "*"
+pystac-client = "*"
+scipy = "*"
+numpy = "1.24.*"
+pandas = "*"
+stackstac = "*"
+geopandas = "*"
+rioxarray = "*"
+rasterio = "1.3.*"
+networkx = "3.3"
+matplotlib = "*"
+typing-extensions = ">=4.12.0rc1"
+sqlite = "*"
+pip = "*"
+
+[target.linux-64.pypi-dependencies]
+mesa = { version = "==3.1.1" }
+mesa-geo = { version = "==0.9.0" }
+networkx = { version = "==3.1" }
+solara = "*"