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 <[email protected]> * 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 <[email protected]> Co-authored-by: lachlangrose <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AngRodrigues <[email protected]> Co-authored-by: Rabii Chaarani <[email protected]> Co-authored-by: rabii-chaarani <[email protected]> Co-authored-by: RoyThomsonMonash <[email protected]>
Loop3D · Dec 16, 2024 · 7978841 · 7978841
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -6,7 +6,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        ## Bug Report
+        ## 🐛 Bug Report
         Thanks for submitting a bug report to map2loop!
         Please use this template to report a bug. Please provide as much detail as possible to help us reproduce and fix the issue efficiently.
 
@@ -16,6 +16,8 @@ body:
       label: Version
       description: What version of map2loop and LoopProjectFile are you running? You can find this information by running `import map2loop` and `map2loop.__version__` in your python terminal or jupyter notebook. 
       placeholder: "Enter map2loop and LoopProjectFile versions"
+    validations:
+      required: true
 
   - type: textarea
     id: bug_description
@@ -33,25 +35,7 @@ body:
       description: "Provide a minimal reproducible example with the code necessary to reproduce the bug. For more guidance, visit: [How to create a minimal complete reproducible example](https://forum.access-hive.org.au/t/how-to-create-a-minimal-complete-reproducible-example/843)"
       placeholder: "Enter the steps to reproduce the bug"
     validations:
-      required: true
-
-  - type: textarea
-    id: expected_behavior
-    attributes:
-      label: "Expected Behavior"
-      description: "Describe what you expected to happen."
-      placeholder: "Enter the expected behavior"
-    validations:
-      required: true
-
-  - type: textarea
-    id: actual_behavior
-    attributes:
-      label: "Actual Behavior"
-      description: "Describe what actually happened when you encountered the bug."
-      placeholder: "Enter the actual behavior"
-    validations:
-      required: true
+      required: false
 
   - type: textarea
     id: additional_context
@@ -69,18 +53,7 @@ body:
       description: "Specify the environment in which the bug occurred (e.g., operating system, browser, application version)."
       placeholder: "Enter the environment details"
     validations:
-      required: true
+      required: false
+
 
-  - type: checkboxes
-    id: severity
-    attributes:
-      label: "Severity"
-      description: "Select the severity level of the bug."
-      options:
-        - label: "Low"
-        - label: "Medium"
-        - label: "High"
-        - label: "Critical"
-    validations:
-      required: true
 
diff --git a/.github/ISSUE_TEMPLATE/documentation_request.yml b/.github/ISSUE_TEMPLATE/documentation_request.yml
@@ -6,8 +6,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        ## Documentation Request
-
+        ## 📓 Documentation Request
         Please use this template to suggest an improvement or addition to map2loop documentation. 
         Provide as much detail as possible to help us understand and implement your request efficiently
 
@@ -18,13 +17,4 @@ body:
       description: "Describe the documentation you would like to see. Include details on why it is needed and how it should be structured."
       placeholder: "Enter a detailed description of the documentation"
     validations:
-      required: true
-
-  - type: textarea
-    id: additional_context
-    attributes:
-      label: "Additional Context"
-      description: "Any other context or information that may be helpful."
-      placeholder: "Enter any additional context"
-    validations:
-      required: false
+      required: true
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -6,8 +6,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        ## Feature Request
-
+        ## 🚀 Feature Request
         Please use this template to submit your feature request. Provide as much detail as possible to help us understand and implement your request efficiently.
 
   - type: checkboxes
@@ -29,50 +28,12 @@ body:
     validations:
       required: true
 
-  - type: textarea
-    id: current_situation
-    attributes:
-      label: "Current Situation"
-      description: "Describe the current situation and how the absence of this feature affects you."
-      placeholder: "Explain the current situation and its drawbacks"
-    validations:
-      required: true
-
   - type: textarea
     id: version
     attributes:
       label: Version
       description: What version of map2loop and LoopProjectFile are you running that doesn't have this feature? You can find this information by running `import map2loop` and `map2loop.__version__` in your python terminal or jupyter notebook. 
       placeholder: "Enter map2loop and LoopProjectFile versions"
-
-  - type: textarea
-    id: proposed_solution
-    attributes:
-      label: "Proposed Solution"
-      description: "Describe how you envision the feature working. Include any specific requirements or details"
-      placeholder: "Explain how the feature should work"
     validations:
       required: true
 
-  - type: input
-    id: additional_context
-    attributes:
-      label: "Additional Context"
-      description: "Provide any other context or information that may be helpful in understanding the feature request."
-      placeholder: "Enter any additional context"
-    validations:
-      required: false
-
-  - type: checkboxes
-    id: affected_areas
-    attributes:
-      label: "Affected Areas"
-      description: "Select the areas of the project that this feature request impacts."
-      options:
-        - label: "input data"
-        - label: "project creation"
-        - label: "samplers"
-        - label: "sorters"
-        - label: "stratigraphic column"
-        - label: "data types"
-        - label: "Other"
diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml
@@ -6,8 +6,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        ## Question
-
+        ## 💬 Question
         Please use this template to ask a question about applying map2loop to your data. 
         Provide as much detail as possible to help us understand and answer your question efficiently.
 
@@ -29,11 +28,11 @@ body:
     validations:
       required: false
 
-  - type: input
+  - type: textarea
     id: additional_context
     attributes:
       label: "Additional Context"
       description: "Provide any other context or information that may be helpful in answering your question."
       placeholder: "Enter any additional context"
     validations:
-      required: false
+      required: false