Update packaging to use 'pyproject.toml'

README.rst

@@ -9,9 +9,9 @@
 environment
 ===========
 
-First, download this code::
+First, download/clone the repository::
 
-    git clone https://github.com/larpix/ndlar_flow
+    git clone https://github.com/DUNE/ndlar_flow
 
 venv method (recommended)
 -------------------------
@@ -21,46 +21,28 @@ Create and activate a virtual environment::
     python -m venv ndlar_flow.venv
     source ndlar_flow.venv/bin/activate
 
-Install the ``h5flow`` framework::
-
-    git clone https://github.com/larpix/h5flow
-    cd h5flow
-    pip install -e .
-    cd ..
-
-Finally, install ``ndlar_flow``::
+Install ``ndlar_flow``::
 
     cd ndlar_flow
     pip install -e .
 
 Note that the ``-e`` option installs the packages in "editable" mode, meaning
 any changes you make will take effect without the need to re-run ``pip install``.
 
-The next section describes the older setup procedure based on ``conda``. The
-comments regarding MPI are historical; h5flow's MPI support is slated to be
-removed in the future.
-
-conda method (deprecated)
--------------------------
-
-To install proper dependencies, use the provided conda environment file ``env.yaml``::
-
-    conda env create -f env.yaml -n <environment name>
-    conda activate <environment>
-
-To update an existing environment::
+legacy install notes
+--------------------
 
-    conda env update -f env.yaml -n <environment name>
+Previous versions of ndlar-flow assumed h5flow was already installed or available
+in the current environment. 
 
-If MPI is not available, you may use the alternative environment file
-(``env-nompi.yaml``) that does not install parallel-HDF5. The ``ndlar_flow`` code
-is built off of ``h5flow`` [https://github.com/larpix/h5flow], so you
-will also need to install this in order to run any of the workflows described
-here.
+To install h5flow manually::
 
-To install::
+    git clone https://github.com/DUNE/h5flow
+    cd h5flow
+    pip install -e .
+    cd ..
 
-    pip install .
+Be sure this is in the same (virtual) environment as ndlar-flow.
 
 usage
 =====

pyproject.toml

@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools>=64.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ndlar_flow"
+description = "An h5flow-based analysis framework for DUNE ND-LAr simulation and data"
+readme = { file = "README.rst", content-type = "text/x-rst" }
+authors = [
+    { name = "Peter Madigan" }
+]
+maintainers = [
+    { name = "Yifan Chen" },
+    { name = "Matt Kramer" },
+    { name = "Noe Roy" },
+    { name = "Kevin Wood" },
+]
+requires-python = ">=3.7"
+license = "Apache-2.0"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Physics"
+]
+dynamic = ["version"]
+dependencies = [
+    "h5py>=2.10",
+    "pytest",
+    "scipy",
+    "scikit-image",
+    "scikit-learn>=1.3.0",
+    "dbscan1d==0.2.3",
+    "h5flow @ git+https://github.com/DUNE/h5flow.git#egg=h5flow",
+    "pylandau @ git+https://github.com/SiLab-Bonn/pylandau.git",
+    "adc64format @ git+https://github.com/larpix/adc64format.git@v0.1.5#egg=adc64format",
+]
+
+[tool.setuptools.dynamic]
+version = { file = "VERSION" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+line-length = 100
+indent-width = 4
+
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
+line-ending = "auto"
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle
+    "F",   # Pyflakes
+    "UP",  # pyupgrade
+    "B",   # flake8-bugbear
+    "SIM", # flake8-simplify
+    "I",   # isort
+]
+ignore = ["E501"]
+
+[tool.mypy]
+disable_error_code = ["import-untyped"]

test/env-nompi.yaml

@@ -14,4 +14,4 @@ dependencies:
   - pip:
     - pyyaml-include==1.3.2
     - adc64format>=0.0.2
-    - git+https://github.com/cuddandr/pylandau.git@npy_owndata_fix
+    - git+https://github.com/SiLab-Bonn/pylandau.git

test/env.yaml

@@ -20,4 +20,4 @@ dependencies:
     - pyyaml-include==1.3.2
     - h5py --no-binary=h5py
     - adc64format>=0.0.2
-    - git+https://github.com/cuddandr/pylandau.git@npy_owndata_fix
+    - git+https://github.com/SiLab-Bonn/pylandau.git