Common base class

README.rst

@@ -24,7 +24,7 @@ Installation
 
    $ pip install springcraft
 
-or 
+or
 
 .. code-block:: console
 
@@ -41,12 +41,22 @@ via *pip*:
    $ git clone https://github.com/biotite-dev/springcraft.git
    $ pip install ./springcraft
 
-A development conda environment with all required dependencies for testing
-can be installed from `environment.yml`
+Development
+-----------
 
-Scripts to generate reference files for tests are stored in tests/data; 
+For development and testing first create a conda enviroment from the
+`environment.yml` and than let poetry install the required dependencies.
+
+.. code-block:: console
+
+   $ conda env create -f environment.yml
+   $ conda activate springcraft-dev
+   $ poetry config virtualenvs.create false
+   $ poetry install
+
+Scripts to generate reference files for tests are stored in tests/data;
 a separate environment to rerun these locally can be found in `test_create_data_env.yml`.
-BioPhysConnectoR has to be installed separately. 
+BioPhysConnectoR has to be installed separately.
 
 Example
 =======
@@ -91,4 +101,4 @@ Output:
     [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0.  0.  0. -1.  4. -1. -1.  0.]
     [ 0.  0.  0.  0.  0. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1. -1.]
     [ 0. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1.]
-    [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  2.]]
+    [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  2.]]

doc/apidoc.rst

@@ -13,12 +13,14 @@ Network models
 
 .. autoclass:: GNM
    :members:
+   :inherited-members:
 
 |
 
 .. autoclass:: ANM
    :members:
-
+   :inherited-members:
+
 |
 
 
@@ -56,4 +58,4 @@ Miscellaneous
 
 .. autofunction:: compute_kirchhoff
 
-.. autofunction:: compute_hessian
+.. autofunction:: compute_hessian

environment.yml

@@ -1,20 +1,12 @@
-# Conda environment, that includes all packages that are necessary for
-# the complete Biotite development process.
-
+# Coda environment to facilitate Biotite development process.
+# After creating the environment install the required packages with
+#   poetry config virtualenvs.create false
+#   poetry install
 name: springcraft-dev
 
 channels:
   - conda-forge
 
 dependencies:
-  - numpy >=2.0
-  - biotite >=1.0.1
-  - pytest >=5.2
-  - matplotlib >=3.3
-  - poetry >=1.0
-  - jinja2 <3.1
-  - sphinx >=3.0
-  - sphinx-gallery =0.9.0
-  - numpydoc >=0.8
-  - ammolite >=0.8
-  - ruff >=0.6.7
+  - poetry
+  - python=3.11

pyproject.toml

@@ -34,19 +34,22 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.10"
-biotite = ">= 0.32"
-numpy = ">= 1.25"
+python = ">=3.10,<4.0"
+biotite = ">=1.0"
+numpy = ">=2.0"
 
-[tool.poetry.dev-dependencies]
-biotite = ">= 1.0"
-pytest = "^5.2"
-sphinx = "^3.0"
-sphinx-gallery = "0.9.0"
-numpy = ">= 2.0"
-numpydoc = ">= 0.8"
-ammolite = ">=0.8"
+[tool.poetry.group.dev.dependencies]
+pytest = ">=8.0"
 ruff = ">=0.6.7"
+pytest-cov = "^7.1.0"
+
+[tool.poetry.group.docs.dependencies]
+ammolite = ">=0.8"
+jinja2 = ">=3.1"
+matplotlib = ">=3.3"
+numpydoc = ">=0.8"
+sphinx = ">=3.0"
+sphinx-gallery = ">=0.9.0"
 
 [build-system]
 requires = ["poetry_core>=1.0.0"]
@@ -60,8 +63,8 @@ ignore = [
     # Most other ocassions are caught by the ruff formatter
     "E501",
     # camel cases for forcefields
-    "N802", 
-    # eANM/sdENM as static methods of TabulatedForceField 
+    "N802",
+    # eANM/sdENM as static methods of TabulatedForceField
     # should not accept "self" as argument by design
     "N805",
     # Due to constants used in functions
@@ -74,4 +77,4 @@ ignore = [
 
 [tool.pytest.ini_options]
 # Pytest: Ignore Python scripts for reference data creation
-addopts =  "--ignore=tests/data"
+addopts =  "--ignore=tests/data"