feat: v3.2 (#153)

* Update issue templates

* feat: added issue_templates

* fix: add pull request template

* fix: few typos grammar

* fix: tests should be with pytest

* Revert "Update issue templates"

* fix: trigger build

* style: style fixes by ruff and autoformatting by black

* chore(master): release 3.1.1

* fix: update doc deploy

* chore(master): release 3.1.2

* docs: remove lavavu; no need for 3D vis for the examples

* style: style fixes by ruff and autoformatting by black

* fix: remove tini from docker

* chore(master): release 3.1.3

* Update issue templates

* feat: added issue_templates

edit dddf70b chore: added issue_templates

* fix: add pull request template

* fix: few typos grammar

* fix: tests should be with pytest

* Revert "Update issue templates"

* fix: add issue templates back

* fix: correct grammar for clarity

* fix: squashed commits of: - fixing the non-use of minimum_fault_length, - use tmpfile to create temporary files, - added random test for mapdata functions:get/set working projection, - added functionality and comments to basal_contacts_build

* tests: add more functionality

* fix: leave as is for now

* fix: finalise the thickness calculator outputs

* fix: Remove hjson and rely on json only

* fix: update tests/ small fixes

* fix: make sure dependencies are right

* fix: linting issue

* fix: try again

* fix: update thickness tests//fix minor typos

* fix: correct some typos/update tests

* fix: typo in tests

* Update README.md

* fix: add the basal_contacts_abnormal_check

* fix: add error handles for json, url, filenotfound

* fix: remove typo

* fix: remove tqdm

* fix: added check for collocated points

* fix: upd gdal as per master

* fix: remove test from server

* fix: issue 122

* fix: update str format

* fix: now use DBSCAN to aggregate collocated poins

* fix: removed addition

* fix: added warning when collocated points detected

* fix: add str for paths - gdal does not accept pathlibs

* fix: update minimum_fault_length as per code review

* fix: add pathlibs where possible in m2model_wrapper

* fix: add pathlib in mapdata.py

* fix: revert pathlib in map2model.run

* fix: proj should not have temp files

* fix: update the minimum_fault_length

* tests: add tests for minimum_fault_length

* fix: remove redundancy from project.py

* fix: update calculate minimum_fault_length for 5% of the map area

* fix: linting

* fix: typo

* fix: remove repetitive print stat

* fix: adjust thickness_calc workflow for modularity

* fix: remove unnecessary fields

* fix: update thickness tests

* fix: add ignore_fault_codes and tests for ignore_lithology_code and ignore_fault_code

* fix: try relative path ../_datasets

* fix: use only path instead of pkg_resources

* fix: try full path

* fix: load only using path /hamersley

* fix: try ./map2loop/_datasets/geodata_files/

* fix: use correct path

* refactor: back to original code

* fix: add the whole hamersley folder

* fix: update docker for docs

* fix: update the docs-deploy for master branch only

* fix: update CI to build on master only

* fix: remove redundancy

* fix: update the server test and handle timeout properly

* fix: updated ReadMe to have the right install steps (temporary measure)

* fix: update CI - test wheels on master only

* fix: add test to sdist build in CI to ensure tests are run in the non-master branches

* fix: update pytest in ci

* fix: revert ci

* fix: add pytest in the right place

* fix: update pytest location

* fix: manifest update

* fix: update ci again

* investigate

* find the install folder

* try again

* update ci

* fix: add checkout step to build sdist

* fix: run pytest with test sdist action

* fix: revert CI and let tests only run on main branch

* fix: add version check new class to check install of  dependencies.txt; includes version number check

* fix: organise manifest

* fix: linting fixes from merges

* fix: update CI to run all jobs on branch

* fix: update map2model paths

* fix: update LPF to install from branch

* fix: update install from branch

* fix: update the lpf to branch in wheel testing

* fix: build the docs on this branch

* fix: keep docs separate

* fix: pypi and conda upld runs only on master

* fix: test the docs on the branch too

* fix: update docs docker to build lpf from branch

* fix: install sphinx with apt-get?

* docs: change sphinx build path

* fix: update build path docs

* docs: update build requirements

* fix: add beartype

* docs: typo in docker?

* fix: remove redundant beartpe install

* chore: typo

* fix: simplify issue templates

* chore: hjson not in 3.2

* fix: remove hjson from dependencies as not in 3.2

* doc: removing min fault length attribute docstring

* fix: adding min fault length setter back to project. Linking to config attribute

* fix: min fault length setter/getter for mapdata uses config attribute

* No data min fault length is -1

* chore: test unpin gdal from ci

* fix: remove sphinx from docs docker build

* chore: try again

* fix: map2model fault fault relationships (#140)

* fix: fault topology merge was using incorrect lookups

* fix: run map2model for user defined stratigraphic column

* removing logger from this pr

* fix: use fault id not Fault_{id}

* feat: make map2model optional using geopandas spatial joins as a replacement (#154)

* fix: stratigraphic alpha sorter was inverted, reverse sorter

* ignore units without contact for max contact length sorter

* updated orientation sorter to use correct trigonometry for strike/dip lines.

also change to using all intersections along line not only the first intersection. perhaps this should be a different sorter?

* revert back to original orientation sorter

* style: black

* updating WA json to work

* remove unused argument documentation

* only run doc build on master

* use geopandas to produce topology graphs instead of map2model.

Basically just using sjoins and buffers. Returns the same for faults and contacts but
we have some differences for fault-unit intersections.

* update sorter to not use stratigraphic order hint and deprecate hint sorter

* update deformation history to use eventId not name for merging

* bipass old map2model run

* use property accessor to make sure that variables are up to date

* remove sorted units from sorter call

* removing comment and condaforge channel

* fix: remove map2model call from map2loop

this is a quick fix, and needs to be cleaned up as the tmp files for map2model are still being created
and the old code is just commented

* update networkx sorter to have a name2index map

* fix: add mode to choose betweeen m2m and geopandas

* remove gdal fix

* linting

* style: black formatting

* fix: make the minimum_fault_length updatable through project

* fix: add libgdal to docs docker

* typo

* fix: try other gdal on docs

* more gdal issues

* fix: revert the gdal pin removal to see if that's the issue

* fix: use minimum fault length from project

* fix: use separate thickness table in LPF & add active thickness to project (#157)

* fix: use separate thickness table in LPF

* docs: remove unused docstring

* fix: min fault length can be int

* fix: bug in output of StructuralPoint

* fix: add the active_thickness_flag

---------

Co-authored-by: AngRodrigues <angela.rodrigues@monash.edu>

* feat: do not accept any legacy files

* chore: small typo

* remove legacy format arguments

* add config file path back

* fix: allow json files, check for old keys

* chore: add/fix/update logger outputs

* chore: more logging

* chore: update tests to not rely on warnings

* chore: proper string formatting

* fix: small fixes for deprecation/linting warnings in test sessions

* chore: update actions from deprecation

* fix: issue 155  (#158)

* fix: simple fix for #155

* fix: decimation factor allows floats

* fix: decimation int

* fix: remove print statement left behind

* chore: update docstrings

* fix: gdal: test if conda issue

* fix: revert

* remove gdal pin??

* fix: keep gdal pin for now

* fix: add debug info to thickness calculators (#161)

* fix: initial commit

* fix: add debug info and warning for bad calculations

* fix: add line length control to thickness calculators

* fix: refactor to avoid repetitive code

* fix: typo

* fix: remove list comprehension - wky

* fix list to df

* fix: revert to lst comprehension

* fix: make line length attribute of the TC class

* fix: typos

* fix: syntax

* fix: add location tracking

* fix: init commit to remove lst comprehension

* chore: empty commit to trigger ci run

* chore: update typing to avoid deprecation

* fix: update ubuntu

* ci: small updates

* fix: dependencies updated

* fix: update LPF dependency

* fix: update linting and release-please

* ci: typos

* ci: keep release-please separate from linting

* ci: update testing

* ci: add pytest

* ci: update testing workflow

* ci: update linting action

* chore: upd conda meta

* style: style fixes by ruff and autoformatting by black

* ci: add conda & pypi

* ci: add docs

* ci: update to ubuntu24.04

* ci: force docs to branch gh ref

* chore: add testing badge to readme

* chore: add release badge

* Update README.md

* Update README.md

* fix: update conda and pip builds

* ci: add classic solver

* ci: add extra action to test conda build and install

* ci update

* ci: update

* gdal pin?

* add libmamba

* chore: typos

* Fix: update gdal install in actions (#163)

* ci: remove the build test for now

---------

Co-authored-by: Lachlan Grose <lachlan.grose@monash.edu>
Co-authored-by: lachlangrose <lachlangrose@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AngRodrigues <AngRodrigues@users.noreply.github.com>
Co-authored-by: Rabii Chaarani <50892556+rabii-chaarani@users.noreply.github.com>
Co-authored-by: rabii-chaarani <rabii.chaarani@monash.edu>
Co-authored-by: RoyThomsonMonash <roy.thomson@monash.edu>

Author: 5 people

.github/workflows/conda.yml

@@ -11,7 +11,11 @@ jobs:
       fail-fast: false
       matrix:
         os: ${{ fromJSON(vars.BUILD_OS)}}
+<<<<<<< HEAD
         python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
+=======
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
+>>>>>>> 7978841 (feat: v3.2 (#153))
     steps:
       - uses: conda-incubator/setup-miniconda@v3
         with:
@@ -27,6 +31,7 @@ jobs:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
         shell: bash -l {0}
         run: |
+<<<<<<< HEAD
           conda config --env --add channels conda-forge 
           conda config --env --add channels loop3d
           conda config --env --set channel_priority strict
@@ -35,6 +40,12 @@ jobs:
           conda build --output-folder conda conda  --python ${{matrix.python-version}}
           anaconda upload --label main conda/*/*.tar.bz2
 
+=======
+          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}}
+          anaconda upload --label main conda/*/*.tar.bz2
+
+>>>>>>> 7978841 (feat: v3.2 (#153))
       - name: upload artifacts
         uses: actions/upload-artifact@v4
         with:

.github/workflows/linting_and_testing.yml

@@ -18,8 +18,12 @@ jobs:
       - uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "style: style fixes by ruff and autoformatting by black"
+<<<<<<< HEAD
 
 
+=======
+
+>>>>>>> 7978841 (feat: v3.2 (#153))
   testing:
     name: Testing
     runs-on: ubuntu-24.04

.github/workflows/pypi.yml

@@ -6,7 +6,11 @@ jobs:
 
   sdist:
     name: Build sdist
+<<<<<<< HEAD
     runs-on: ubuntu-latest
+=======
+    runs-on: ubuntu-24.04
+>>>>>>> 7978841 (feat: v3.2 (#153))
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -23,7 +27,11 @@ jobs:
 
   publish:
     name: Publish wheels to pypi
+<<<<<<< HEAD
     runs-on: ubuntu-latest
+=======
+    runs-on: ubuntu-24.04
+>>>>>>> 7978841 (feat: v3.2 (#153))
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write

MANIFEST.in

@@ -1,3 +1,12 @@
+include LICENSE
+include README.md 
+
 include map2loop/_datasets/clut_files/*.csv
 include map2loop/_datasets/config_files/*.json
-include map2loop/_datasets/geodata_files/hamersley/*
+<<<<<<< HEAD
+include map2loop/_datasets/geodata_files/hamersley/*
+=======
+include map2loop/_datasets/geodata_files/hamersley/*
+
+recursive-include tests *.py
+>>>>>>> 7978841 (feat: v3.2 (#153))

README.md

@@ -1,18 +1,22 @@
 ![GitHub Release](https://img.shields.io/github/v/release/loop3d/map2loop)
 <<<<<<< HEAD
 <<<<<<< HEAD
+<<<<<<< HEAD
 [![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)
 =======
 >>>>>>> 7978841 (feat: v3.2 (#153))
 =======
 [![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)
 >>>>>>> c1060e5 (chore: update readme)
+=======
+>>>>>>> 7978841 (feat: v3.2 (#153))
 ![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)
 
+<<<<<<< HEAD
 <<<<<<< HEAD
 <<<<<<< HEAD
 
@@ -24,6 +28,9 @@
 
 # Map2Loop 3.2
 >>>>>>> c1060e5 (chore: update readme)
+=======
+# Map2Loop 3.1
+>>>>>>> 7978841 (feat: v3.2 (#153))
 
 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:
 
@@ -76,12 +83,20 @@ conda install -c loop3d -c conda-forge --file dependencies.txt
 pip install .
 ```
 
+<<<<<<< HEAD
 #### Option 4: From source & developer mode:
+=======
+### Run
+
+To just use map2loop, issue the following. <sup>*</sup>
+
+>>>>>>> 7978841 (feat: v3.2 (#153))
 ```bash
 git clone https://github.com/Loop3D/map2loop.git
 
 cd map2loop
 
+<<<<<<< HEAD
 conda install gdal
 
 conda install -c loop3d -c conda-forge --file dependencies.txt
@@ -115,6 +130,14 @@ conda install -c loop3d -c conda-forge --file dependencies.txt
 pip install -e .
 ```
 >>>>>>> c1060e5 (chore: update readme)
+=======
+conda install -c loop3d --file dependencies.txt
+
+pip install .
+```
+
+<p><sup>*</sup> We're actively working towards a better approach - stay tuned! </p>
+>>>>>>> 7978841 (feat: v3.2 (#153))
 
 ### Documentation
 

conda/conda_build_config.yaml

@@ -0,0 +1,6 @@
+python:
+  - 3.8
+  - 3.9
+  - 3.10
+  - 3.11
+  - 3.12

conda/meta.yaml

@@ -7,8 +7,13 @@ package:
 source:
   git_url: https://github.com/Loop3D/map2loop
 
+
 build:
   number: 0
+<<<<<<< HEAD
+=======
+  script: "{{ PYTHON }} -m pip install . --no-deps"  
+>>>>>>> 7978841 (feat: v3.2 (#153))
 
 requirements:
   host:
@@ -18,17 +23,26 @@ requirements:
   run:
     - loopprojectfile ==0.2.2
     - gdal
+<<<<<<< HEAD
+=======
+    - map2model
+    - beartype
+>>>>>>> 7978841 (feat: v3.2 (#153))
     - python
     - numpy
     - scipy
     - geopandas
     - shapely
     - networkx
     - owslib
+<<<<<<< HEAD
     - map2model
     - beartype
     - pytest
     - scikit-learn
+=======
+
+>>>>>>> 7978841 (feat: v3.2 (#153))
 
 about:
   home: "https://github.com/Loop3D/map2loop"

dependencies.txt

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

map2loop/__init__.py

@@ -30,7 +30,11 @@ class DependencyChecker:
 
     def __init__(self, package_name, dependency_file="dependencies.txt"):
         self.package_name = package_name
+<<<<<<< HEAD
         self.dependency_file = pathlib.Path(__file__).parent / dependency_file
+=======
+        self.dependency_file = pathlib.Path(__file__).parent.parent / dependency_file
+>>>>>>> 7978841 (feat: v3.2 (#153))
         self.required_version = self.get_required_version()
         self.installed_version = self.get_installed_version()
 
@@ -93,7 +97,11 @@ def check_version(self):
 
 
 def check_all_dependencies(dependency_file="dependencies.txt"):
+<<<<<<< HEAD
     dependencies_path = pathlib.Path(__file__).parent / dependency_file
+=======
+    dependencies_path = pathlib.Path(__file__).parent.parent / dependency_file
+>>>>>>> 7978841 (feat: v3.2 (#153))
     try:
         with dependencies_path.open("r") as file:
             for line in file:
@@ -108,7 +116,10 @@ def check_all_dependencies(dependency_file="dependencies.txt"):
 
                     checker = DependencyChecker(package_name, dependency_file=dependency_file)
                     checker.check_version()
+<<<<<<< HEAD
 
+=======
+>>>>>>> 7978841 (feat: v3.2 (#153))
     except FileNotFoundError:
         warnings.warn(
             f"{dependency_file} not found. No dependencies checked for map2loop.",

pyproject.toml

@@ -38,11 +38,15 @@ version = { attr = "map2loop.version.__version__" }
 [tool.setuptools.packages.find]
 include = ['map2loop', 'map2loop.*']
 
+<<<<<<< HEAD
 [tool.setuptools.package-data]
 map2loop = [
     "dependencies.txt",
     "_datasets/geodata_files/hamersley/*"
 ]
+=======
+
+>>>>>>> 7978841 (feat: v3.2 (#153))
 
 [tool.black]
 line-length = 100