Refactor installation to use pyproject.toml

RNA-FRETools · Oct 28, 2024 · 07923b3 · 07923b3
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commit 07923b3
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Showing 18 changed files with 977 additions and 43 deletions.
diff --git a/__about__.py b/__about__.py
diff --git a/poetry.lock b/poetry.lock
diff --git a/pypam/__init__.py b/pypam/__init__.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,39 @@
+[tool.poetry]
+name = "pamtools"
+version = "0.1.0"
+description = "Visualization tools for the 'PIE Analysis with MATLAB' (PAM) software package"
+authors = ["Fabio Steffen <[email protected]>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://rna-fretools.github.io/"
+repository = "https://github.com/fdsteffen/PAMtools"
+documentation = "https://rna-fretools.github.io/pamtools/"
+keywords = ["PIE", "FRET", "TCSPC", "confocal imaging", "fluorescence", "spectroscopy"]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Matlab",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+[tool.poetry.dependencies]
+python = ">=3.9"
+pandas = "^2.2.3"
+matplotlib = "^3.9.2"
+seaborn = "^0.13.2"
+naturalcolors = "^1.0.2"
+phconvert = "^0.9.1"
+scipy = [
+    {version = "<1.14.1", python = ">=3.9,<3.10"},
+    {version = ">=1.14.1", python = ">=3.10"}
+]
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+
+[tool.black]
+line-length = 120
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
diff --git a/matpam/extract_2Dplot.m → src/pamtools/matpam/extract_2Dplot.m b/matpam/extract_2Dplot.m → src/pamtools/matpam/extract_2Dplot.m
diff --git a/matpam/extract_timetrace.m → src/pamtools/matpam/extract_timetrace.m b/matpam/extract_timetrace.m → src/pamtools/matpam/extract_timetrace.m
diff --git a/matpam/irf/ErythrosinB.irf → src/pamtools/matpam/irf/ErythrosinB.irf b/matpam/irf/ErythrosinB.irf → src/pamtools/matpam/irf/ErythrosinB.irf
diff --git a/matpam/irf/scatter.scat → src/pamtools/matpam/irf/scatter.scat b/matpam/irf/scatter.scat → src/pamtools/matpam/irf/scatter.scat
diff --git a/matpam/models/FCS_D_2trip_nogamma.txt → ...ols/matpam/models/FCS_D_2trip_nogamma.txt b/matpam/models/FCS_D_2trip_nogamma.txt → ...ols/matpam/models/FCS_D_2trip_nogamma.txt
diff --git a/matpam/models/FCS_D_nogamma_green.txt → ...ols/matpam/models/FCS_D_nogamma_green.txt b/matpam/models/FCS_D_nogamma_green.txt → ...ols/matpam/models/FCS_D_nogamma_green.txt
diff --git a/matpam/models/FCS_D_nogamma_red.txt → ...tools/matpam/models/FCS_D_nogamma_red.txt b/matpam/models/FCS_D_nogamma_red.txt → ...tools/matpam/models/FCS_D_nogamma_red.txt
diff --git a/matpam/profiles/PIE.mat → src/pamtools/matpam/profiles/PIE.mat b/matpam/profiles/PIE.mat → src/pamtools/matpam/profiles/PIE.mat
diff --git a/matpam/write_FCS.m → src/pamtools/matpam/write_FCS.m b/matpam/write_FCS.m → src/pamtools/matpam/write_FCS.m
diff --git a/src/pamtools/pypam/__init__.py b/src/pamtools/pypam/__init__.py
@@ -0,0 +1 @@
+from .pamplot import *
diff --git a/pypam/pamplot.py → src/pamtools/pypam/pamplot.py b/pypam/pamplot.py → src/pamtools/pypam/pamplot.py
diff --git a/pypam/photon.py → src/pamtools/pypam/photon.py b/pypam/photon.py → src/pamtools/pypam/photon.py