Merge branch 'master' of https://github.com/Loop3D/map2loop into fix/…

…add_data_checks

.github/workflows/conda.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ${{ fromJSON(vars.BUILD_OS)}}
-        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
     steps:
       - uses: conda-incubator/setup-miniconda@v3
         with:
@@ -27,10 +27,14 @@ jobs:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
         shell: bash -l {0}
         run: |
+          conda config --env --add channels conda-forge 
+          conda config --env --add channels loop3d
+          conda config --env --set channel_priority strict
           conda install -c conda-forge conda-build scikit-build-core numpy anaconda-client conda-libmamba-solver -y
-          conda build -c conda-forge -c loop3d --output-folder conda conda  --python ${{matrix.python-version}}reve
+          conda config --set solver libmamba
+          conda build --output-folder conda conda  --python ${{matrix.python-version}}
           anaconda upload --label main conda/*/*.tar.bz2
-
+          
       - name: upload artifacts
         uses: actions/upload-artifact@v4
         with:

.github/workflows/linting_and_testing.yml

@@ -18,7 +18,8 @@ jobs:
       - uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "style: style fixes by ruff and autoformatting by black"
-
+
+
   testing:
     name: Testing
     runs-on: ubuntu-24.04

.github/workflows/pypi.yml

@@ -6,7 +6,7 @@ jobs:
 
   sdist:
     name: Build sdist
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -23,7 +23,7 @@ jobs:
 
   publish:
     name: Publish wheels to pypi
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write

.release-please-manifest.json

@@ -1,3 +1,3 @@
 {
-  ".": "3.2.0"
+  ".": "3.2.1"
 }

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [3.2.1](https://github.com/Loop3D/map2loop/compare/v3.2.0...v3.2.1) (2025-01-12)
+
+
+### Bug Fixes
+
+* include dependencies in site-packages  - issue [#169](https://github.com/Loop3D/map2loop/issues/169) ([#170](https://github.com/Loop3D/map2loop/issues/170)) ([b33532b](https://github.com/Loop3D/map2loop/commit/b33532b56473148433fd192e182aadee028dc875))
+
 ## [3.2.0](https://github.com/Loop3D/map2loop/compare/v3.1.13...v3.2.0) (2024-12-16)
 
 

MANIFEST.in

@@ -1,8 +1,3 @@
-include LICENSE
-include README.md 
-
 include map2loop/_datasets/clut_files/*.csv
 include map2loop/_datasets/config_files/*.json
-include map2loop/_datasets/geodata_files/hamersley/*
-
-recursive-include tests *.py
+include map2loop/_datasets/geodata_files/hamersley/*

README.md

@@ -1,100 +1,70 @@
 ![GitHub Release](https://img.shields.io/github/v/release/loop3d/map2loop)
+[![DOI](https://img.shields.io/static/v1?label=DOI&message=10.5194/gmd-14-5063-2021&color=blue)](https://doi.org/10.5194/gmd-14-5063-2021)
 ![License](https://img.shields.io/github/license/loop3d/map2loop)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/map2loop?label=pip%20downloads)
 ![Conda Downloads](https://img.shields.io/conda/dn/loop3d/map2loop?label=Conda%20downloads)
 [![Testing](https://github.com/Loop3D/map2loop/actions/workflows/linting_and_testing.yml/badge.svg)](https://github.com/Loop3D/map2loop/actions/workflows/linting_and_testing.yml)
 [![Build and Deploy Documentation](https://github.com/Loop3D/map2loop/actions/workflows/documentation.yml/badge.svg)](https://github.com/Loop3D/map2loop/actions/workflows/documentation.yml)
 
-# Map2Loop 3.1
+
+# Map2Loop 3.2
 
 Generate 3D geological model inputs from geological maps — a high-level implementation and extension of the original map2loop code developed by Prof. Mark Jessell at UWA. To see an example interactive model built with map2loop and LoopStructural, follow this link:
 
 <a href="http://tectonique.net/models/brockman_syncline.html">3D Model from the Hamersley region, Western Australia</a>
 
 ## Install
 
-You will need some flavour of conda (a Python package manager, [see here](https://docs.anaconda.com/anaconda/install/index.html)), as well as Python ≥ 3.8. 
+#### Option 1: Install with Anaconda
 
-### Adding  ```conda-forge``` to Anaconda channels
-map2loop installation may run smoother if ```conda-forge``` is added to the channels. 
-To check for that, run 
+This is the simplest and recommended installation process, with:
 
 ```bash
-conda config --show channels
+conda install -c loop3d -c conda-forge map2loop
 ```
-if conda-forge is not in the output, the channel can be added with:
 
+#### Option 2: Install with pip
+Installation with pip will require that GDAL is installed on your system prior to map2loop installation. 
+This is because GDAL cannot be installed <a href='https://hackernoon.com/hn-images/1*m4cnTYJWM7Rmpsju8dSHmQ.jpeg'>via pip</a> (at least not with one line of code), and the GDAL installation process will vary depending on your OS. 
+
+For more information on installing gdal, see <a href="https://pypi.org/project/GDAL/">GDAL's Pypi</a> page.
+
+Once GDAL is available on your system, map2loop can be installed with:
 ```bash
-conda config --add channels conda-forge
+pip install map2loop
 ```
 
-### Run
-
-To just use map2loop, issue the following. <sup>*</sup>
+#### Option 3: From source
 
 ```bash
 git clone https://github.com/Loop3D/map2loop.git
 
 cd map2loop
 
-conda install -c loop3d --file dependencies.txt
+conda install gdal
+
+conda install -c loop3d -c conda-forge --file dependencies.txt
 
 pip install .
 ```
 
-<p><sup>*</sup> We're actively working towards a better approach - stay tuned! </p>
-
-### Documentation
-
-If you can call it that, is available <a href="https://loop3d.org/map2loop/">here</a>
-
-### Development
-
-If you want to tinker yourself/contribute, clone the source code with
-
+#### Option 4: From source & developer mode:
 ```bash
 git clone https://github.com/Loop3D/map2loop.git
-```
 
-Or get the source + example notebooks with
+cd map2loop
 
-```bash
-git clone https://github.com/Loop3D/map2loop.git
-git clone https://github.com/Loop3D/map2loop-3-notebooks
-```
+conda install gdal
 
-Navigate into map2loop, and issue the following to install map2loop and its dependencies. _Note_: The 'develop' flag makes your source changes take effect on saving, so you only need to run this once
+conda install -c loop3d -c conda-forge --file dependencies.txt
 
-```bash
-conda install -c loop3d --file dependencies.txt
 pip install -e .
 ```
 
-## Building with Docker
-
-Fair warning, we recommend conda to almost everyone. With great software development power comes great environment setup inconvenience. You'll need to download and install the [docker containerisation software](https://docs.docker.com/get-docker/), and the docker and docker-compose CLI.
-
-### Development
-
-1. Clone this repo and navigate inside as per above
-2. Run the following and click on the Jupyter server forwarded link to access and edit the notebooks
-
-   ```bash
-   docker-compose up --build
-   ```
-
-3. To hop into a bash shell in a running container, open a terminal and issue
-
-   ```bash
-   docker ps
-   ```
+### Documentation
 
-   Find the container name or ID and then run
+Map2loop's documentation is available <a href="https://loop3d.org/map2loop/">here</a>
 
-   ```bash
-   docker exec -it <container_NAMEorID> bash
-   # Probably -> docker exec -it  map2loop_dev_1 bash
-   ```
 
 ## Usage
 
@@ -118,8 +88,6 @@ bbox_3d = {
 }
 ```
 
-![sa example](docs/Untitled.png?raw=true)
-
 Then, specify: the state, directory for the output, the bounding box and projection from above - and hit go! That's it.
 
 ```python

conda/bld.bat

@@ -0,0 +1,5 @@
+mkdir %SP_DIR%\map2loop
+copy %RECIPE_DIR%\..\LICENSE %SP_DIR%\map2loop\
+copy %RECIPE_DIR%\..\README.md %SP_DIR%\map2loop\
+copy %RECIPE_DIR%\..\dependencies.txt %SP_DIR%\map2loop\
+%PYTHON% -m pip install . 

conda/build.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+mkdir -p $SP_DIR/map2loop
+cp $RECIPE_DIR/../dependencies.txt $SP_DIR/map2loop/
+cp $RECIPE_DIR/../LICENSE $SP_DIR/map2loop/
+cp $RECIPE_DIR/../README.md $SP_DIR/map2loop/
+$PYTHON -m pip install . 

conda/meta.yaml

@@ -7,10 +7,8 @@ package:
 source:
   git_url: https://github.com/Loop3D/map2loop
 
-
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install . --no-deps"  
 
 requirements:
   host:
@@ -20,17 +18,17 @@ requirements:
   run:
     - loopprojectfile ==0.2.2
     - gdal
-    - map2model
-    - beartype
     - python
     - numpy
-    - pandas
+    - scipy
     - geopandas
     - shapely
-    - tqdm
     - networkx
     - owslib
-
+    - map2model
+    - beartype
+    - pytest
+    - scikit-learn
 
 about:
   home: "https://github.com/Loop3D/map2loop"

dependencies.txt

@@ -1,4 +1,3 @@
-
 numpy
 scipy
 geopandas

map2loop/__init__.py

@@ -30,7 +30,7 @@ class DependencyChecker:
 
     def __init__(self, package_name, dependency_file="dependencies.txt"):
         self.package_name = package_name
-        self.dependency_file = pathlib.Path(__file__).parent.parent / dependency_file
+        self.dependency_file = pathlib.Path(__file__).parent / dependency_file
         self.required_version = self.get_required_version()
         self.installed_version = self.get_installed_version()
 
@@ -93,7 +93,7 @@ def check_version(self):
 
 
 def check_all_dependencies(dependency_file="dependencies.txt"):
-    dependencies_path = pathlib.Path(__file__).parent.parent / dependency_file
+    dependencies_path = pathlib.Path(__file__).parent / dependency_file
     try:
         with dependencies_path.open("r") as file:
             for line in file:
@@ -108,6 +108,7 @@ def check_all_dependencies(dependency_file="dependencies.txt"):
 
                     checker = DependencyChecker(package_name, dependency_file=dependency_file)
                     checker.check_version()
+
     except FileNotFoundError:
         warnings.warn(
             f"{dependency_file} not found. No dependencies checked for map2loop.",