Fixing pip install

.github/workflows/release.yml

@@ -1,57 +1,30 @@
 name: Build and upload to PyPI
 
 on:
-  release:
+ release:
     types:
         - published
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+    name: Build wheels and src
+    runs-on: ubuntu-latest
     steps:
-
-      - uses: actions/checkout@v3
+      - name: checkout
+        uses: actions/checkout@v3
         with:
           fetch-depth: "0"
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          # List of platforms to build on (incl. Python version)
-          CIBW_BUILD: cp3{8,9,10,11}-manylinux_x86_64 cp3{8,9,10,11}-win_amd64 cp3{8,9,10,11}-macosx_x86_64 cp3{8,9,10,11}-macosx_arm64
-
-          CIBW_BEFORE_BUILD: >
-             pip install numpy Cython scipy joblib
-
-          # Install test dependencies and run tests
-          CIBW_TEST_REQUIRES: pytest joblib
-          CIBW_TEST_COMMAND: >
-            pytest {project}/test
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
-
-  build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Build sdist
-        run: |
-          pip install numpy Cython scipy joblib
-          python setup.py sdist
-
-      - uses: actions/upload-artifact@v3
+      - name: install build
+        run: python -m pip install build pytest --user
+      - name: build wheel
+        run: python -m build --sdist --wheel
+      - name: upload wheel
+        uses: actions/upload-artifact@v3
         with:
-          path: dist/*.tar.gz
+          path: dist/
 
   upload_pypi:
-    needs: [build_wheels, build_sdist]
+    needs: [build_wheels]
     runs-on: ubuntu-latest
     permissions:
       id-token: write

docs/source/usage.rst

@@ -2,5 +2,5 @@ Test
 ====
 
 .. autofunction:: quickBayes.log_likelihood.loglikelihood
-.. autofunction:: quickBayes.fit_engines.scipy_fit_engine.ScipyFitEngine
+.. autofunction:: quickBayes.fitting.scipy_engine.ScipyFitEngine
 .. autofunction:: quickBayes.utils.parallel.parallel

pyproject.toml

@@ -0,0 +1,19 @@
+[build-system]
+requires = ['hatchling']
+build-backend = 'hatchling.build'
+
+[project]
+name = 'quickBayes'
+version = "1.0.0b23"
+requires-python = ">=3.7.1"
+dependencies = ['numpy<2.0.0', 'scipy', 'gofit']
+authors = [{name='Anthony Lim', email='[email protected]'}]
+description = "A Bayesian fitting package used for model selection and grid searches of fits for neutron and muon data."
+keywords=['bayesian', 'fitting', 'QENS', 'muons']
+readme = 'README.md'
+license = {text = 'BSD'}
+
+[project.urls]
+Homepage = "https://quickbayes.readthedocs.io/en/latest/"
+Documentation = "https://quickbayes.readthedocs.io/en/latest/"
+Repository = 'https://github.com/ISISNeutronMuon/quickBayes'

quickBayes-dev.yml

@@ -5,7 +5,7 @@ channels:
 
 dependencies:
   - python =3.11.*
-  - numpy
+  - numpy < 2.0.0
   - scipy
   - pytest
   - pre-commit >=2.15

src/quickBayes/workflows/grid_search/qse_grid_search.py → src/quickBayes/workflow/grid_search/qse_grid_search.py

@@ -1,4 +1,4 @@
-from quickBayes.workflow.grid_template import GridSearchTemplate
+from quickBayes.workflow.grid_search.template import GridSearchTemplate
 from quickBayes.functions.qse_fixed import QSEFixFunction
 from quickBayes.utils.spline import spline
 from numpy import ndarray

src/quickBayes/workflows/model_selection/qse_main.py → src/quickBayes/workflow/model_selection/QSE.py

@@ -1,7 +1,7 @@
 from quickBayes.functions.qse_function import QSEFunction
 from quickBayes.utils.spline import spline
 from quickBayes.utils.general import get_background_function
-from quickBayes.workflow.model_template import ModelSelectionWorkflow
+from quickBayes.workflow.model_selection.template import ModelSelectionWorkflow
 from quickBayes.functions.base import BaseFitFunction
 from quickBayes.utils.crop_data import crop
 

src/quickBayes/workflows/model_selection/qldata_main.py → src/quickBayes/workflow/model_selection/QlData.py

@@ -1,7 +1,7 @@
 from quickBayes.functions.qldata_function import QlDataFunction
 from quickBayes.utils.spline import spline
 from quickBayes.utils.general import get_background_function
-from quickBayes.workflow.model_template import ModelSelectionWorkflow
+from quickBayes.workflow.model_selection.template import ModelSelectionWorkflow
 from quickBayes.functions.base import BaseFitFunction
 from quickBayes.utils.crop_data import crop
 

src/quickBayes/workflows/model_selection/muon_exp_decay_main.py → src/quickBayes/workflow/model_selection/muon_decay.py

@@ -2,7 +2,7 @@
 from quickBayes.functions.exp_decay import ExpDecay
 from quickBayes.utils.general import get_background_function
 from quickBayes.utils.crop_data import crop
-from quickBayes.workflow.model_template import ModelSelectionWorkflow
+from quickBayes.workflow.model_selection.template import ModelSelectionWorkflow
 from quickBayes.functions.base import BaseFitFunction
 from numpy import ndarray
 from typing import Dict, List

test/utils/parallel_test.py

@@ -1,5 +1,5 @@
 import unittest
-from quickBayes.workflow.QSE import qse_data_main
+from quickBayes.workflow.model_selection.QSE import qse_data_main
 from quickBayes.utils.parallel import parallel
 import numpy as np
 import os.path

test/workflows/grid_search/gridSearchTemplate_test.py

@@ -1,10 +1,10 @@
 import unittest
-from quickBayes.workflow.grid_template import GridSearchTemplate
+from quickBayes.workflow.grid_search.template import GridSearchTemplate
 from quickBayes.functions.BG import FlatBG
 from quickBayes.functions.exp_decay import ExpDecay
-from quickBayes.test_helpers.workflows import (gen_grid_search_data,
-                                               FixedBG,
-                                               FixedComposite)
+from quickBayes.test_helpers.workflow_helper import (gen_grid_search_data,
+                                                     FixedBG,
+                                                     FixedComposite)
 
 
 class SimpleWorkflow(GridSearchTemplate):

test/workflows/grid_search/quest_test.py

@@ -1,7 +1,7 @@
 import unittest
 from quickBayes.functions.qse_fixed import QSEFixFunction
 from quickBayes.functions.BG import LinearBG
-from quickBayes.workflow.qse_search import QSEGridSearch
+from quickBayes.workflow.grid_search.qse_grid_search import QSEGridSearch
 import numpy as np
 import os.path
 

test/workflows/model_selection/modelSelectionTemplate_test.py

@@ -1,9 +1,9 @@
 import unittest
-from quickBayes.workflow.model_template import ModelSelectionWorkflow
+from quickBayes.workflow.model_selection.template import ModelSelectionWorkflow
 from quickBayes.functions.BG import FlatBG
 from quickBayes.functions.exp_decay import ExpDecay
 from quickBayes.functions.composite import CompositeFunction
-from quickBayes.test_helpers.workflows import gen_model_selection_data
+from quickBayes.test_helpers.workflow_helper import gen_model_selection_data
 
 
 class SimpleWorkflow(ModelSelectionWorkflow):

test/workflows/model_selection/muonexpdecay_test.py → test/workflows/model_selection/muon_decay_test.py

@@ -1,5 +1,5 @@
 import unittest
-from quickBayes.workflow.MuonExpDecay import muon_expdecay_main
+from quickBayes.workflow.model_selection.muon_decay import muon_expdecay_main
 import numpy as np
 import os.path
 

test/workflows/model_selection/qldata_test.py

@@ -1,5 +1,5 @@
 import unittest
-from quickBayes.workflow.QlData import ql_data_main, QLData
+from quickBayes.workflow.model_selection.QlData import ql_data_main, QLData
 from quickBayes.functions.qldata_function import QlDataFunction
 from quickBayes.functions.BG import LinearBG
 import numpy as np

test/workflows/model_selection/qlse_test.py

@@ -1,7 +1,8 @@
 import unittest
 from quickBayes.functions.qse_function import QSEFunction
 from quickBayes.functions.BG import LinearBG
-from quickBayes.workflow.QSE import qse_data_main, QlStretchedExp
+from quickBayes.workflow.model_selection.QSE import (qse_data_main,
+                                                     QlStretchedExp)
 import numpy as np
 import os.path
 

tools/create_conda_yml.py

@@ -81,7 +81,7 @@ def create_default(version):
     default_yml['name'] = 'quickBayes-dev'
     default_yml['channels'] = 'conda-forge'
     default_yml['dependencies'] = {'python': '=' + version + '.*',
-                                   'numpy': '',
+                                   'numpy': '<2.0.0',
                                    'scipy': '',
                                    'pytest': '',
                                    'pre-commit': '>=2.15',