Merge pull request #2 from SECQUOIA/fix-test-codequal

Refactor codebase and enhance CI for quality checks

Author: bernalde

.github/README.md

@@ -36,7 +36,7 @@ A single, comprehensive workflow that replaces multiple separate workflows, redu
 
 ## Triggers
 
-- **Push**: main, master, develop, test-devel branches
+- **Push**: main, master, develop branches
 - **Pull Request**: main, master, develop branches  
 - **Schedule**: Weekly on Sundays at 3 AM UTC
 - **Manual**: Via workflow_dispatch

.github/workflows/ci.yml

@@ -2,7 +2,7 @@ name: PharmaPy CI/CD Pipeline
 
 on:
   push:
-    branches: [ main, master, develop, test-devel ]
+    branches: [ main, master, develop ]
   pull_request:
     branches: [ main, master, develop ]
   schedule:
@@ -157,11 +157,11 @@ jobs:
         python -m pytest tests/integration/test_assimulo.py::TestAssimuloIntegration::test_assimulo_version_compatibility -v
         python -m pytest tests/integration/test_assimulo.py::TestAssimuloIntegration::test_sundials_integration -v
 
-  # Installation script testing - only on push to specific branches
+  # Installation script testing - runs on all pushes
   test-installation-scripts:
     name: Installation Scripts
     timeout-minutes: 20  # Prevent long-running jobs
-    if: github.event_name == 'push' && (contains(github.ref, 'main') || contains(github.ref, 'master') || contains(github.ref, 'test-devel'))
+    if: github.event_name == 'push'
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -195,10 +195,9 @@ jobs:
         conda activate pharmapy-ci-test
         python -c "import PharmaPy; print('Unix script installation successful')"
 
-  # Code quality and documentation - only on main branches
+  # Code quality and documentation - run on every push
   quality-and-docs:
     name: Code Quality & Documentation
-    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
 
     steps:
@@ -220,13 +219,31 @@ jobs:
         pip install -e .
         pip install -r requirements-dev.txt
 
+    - name: Install pandoc (for documentation)
+      shell: bash -l {0}
+      run: |
+        conda install -c conda-forge pandoc --yes
+
+    - name: Install assimulo (for code quality checks)
+      shell: bash -l {0}
+      continue-on-error: true
+      run: |
+        conda install -c conda-forge assimulo --yes || pip install assimulo || echo "Assimulo installation failed, but continuing"
+
     - name: Run linting
       shell: bash -l {0}
       continue-on-error: true
       run: |
         flake8 PharmaPy/ --count --select=E9,F63,F7,F82 --show-source --statistics
         flake8 PharmaPy/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
+    - name: Check code formatting with black
+      shell: bash -l {0}
+      continue-on-error: true
+      run: |
+        echo "Checking code formatting with black..."
+        black --check --diff PharmaPy/ tests/ *.py --exclude="/(\.git|\.venv|\.tox|build|dist|\.eggs)/"
+
     - name: Generate coverage report
       shell: bash -l {0}
       run: |
@@ -258,10 +275,9 @@ jobs:
         name: documentation
         path: doc/_build/html/
 
-  # Build and packaging - only on main branches and releases
+  # Build and packaging - runs on all pushes
   build-and-package:
     name: Build & Package
-    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
     runs-on: ubuntu-latest
 
     steps:

PharmaPy/CheckModule.py

@@ -8,7 +8,6 @@
 import json
 import pathlib
 
-from PharmaPy.Errors import PharmaPySpecificationError
 import warnings
 
 

PharmaPy/Crystallizers.py

@@ -2426,6 +2426,7 @@ def energy_balances(
         vol,
         mu_n,
         h_in,
+        heat_prof=False,
     ):
 
         rho_susp, rho_in = rhos

PharmaPy/Drying_Model.py

@@ -9,18 +9,13 @@
 from assimulo.problem import Explicit_Problem
 from assimulo.solvers import CVode
 import matplotlib.pyplot as plt
-import scipy
 from scipy.interpolate import CubicSpline
 
 from PharmaPy.Phases import classify_phases
-from PharmaPy.MixedPhases import Cake
 from PharmaPy.SolidLiquidSep import high_resolution_fvm, get_sat_inf, upwind_fvm
-from PharmaPy.NameAnalysis import get_dict_states
 
 # from PharmaPy.Interpolation import SplineInterpolation
-from PharmaPy.general_interpolation import define_initial_state
 from PharmaPy.Commons import (
-    reorder_pde_outputs,
     eval_state_events,
     handle_events,
     unpack_discretized,
@@ -483,7 +478,7 @@ def energy_balance(
 
         dTcond_dt = (-drying_terms + heat_transf - heat_loss_cond) / denom_cond
 
-        ## ---- Trial for lumping both cond/gas phase into one
+        # ---- Trial for lumping both cond/gas phase into one
         # dTtotal_dt = (conv_term + sensible_heat - drying_terms - heat_loss_cond)/ (denom_gas + denom_cond)
 
         # dTg_dt, dTcond_dt = dTtotal_dt, dTtotal_dt

PharmaPy/DynamicExtraction.py

@@ -1,19 +1,17 @@
 import numpy as np
-from scipy import linalg
 from scipy.optimize import root
 from assimulo.problem import Implicit_Problem
 
 from PharmaPy.Phases import classify_phases
 from PharmaPy.Connections import get_inputs_new
-from PharmaPy.Commons import unpack_discretized, retrieve_pde_result, flatten_states
+from PharmaPy.Commons import unpack_discretized, retrieve_pde_result
 from PharmaPy.Results import DynamicResult
 from PharmaPy.Streams import LiquidStream
 
 from PharmaPy.Extractors import BatchExtractor
 from PharmaPy.Plotting import plot_distrib
 
 from assimulo.solvers import IDA
-from assimulo.solvers import Radau5DAE
 
 import copy
 

PharmaPy/Evaporators.py

@@ -13,15 +13,14 @@
     unpack_states,
     flatten_states,
 )
-from PharmaPy.Connections import get_inputs, get_inputs_new
+from PharmaPy.Connections import get_inputs_new
 from PharmaPy.Streams import LiquidStream, VaporStream
 from PharmaPy.Phases import LiquidPhase, VaporPhase, classify_phases
 
 from PharmaPy.Results import DynamicResult
 from PharmaPy.Plotting import plot_function
 
 from scipy.optimize import fsolve
-import matplotlib.pyplot as plt
 from matplotlib.ticker import AutoMinorLocator
 
 from assimulo.problem import Implicit_Problem
@@ -1230,7 +1229,7 @@ def plot_profiles(self, pick_comp=None, **fig_kwargs):
             The default is None.
         **fig_kwargs : keyword arguments
             keyword arguments to be passed to the construction of fig and
-            axes object of matplotlib (plt.subplots(**kwargs)).
+            axes object of matplotlib (``plt.subplots(**kwargs)``).
             Do not use nrows or ncols arguments, since the plot grid is already
             defined by PharmaPy
 
@@ -2093,7 +2092,7 @@ def plot_profiles(self, pick_comp=None, vol_plot=False, **fig_kwargs):
             mol_liq-mol_vap vs t is plotted.
         **fig_kwargs : keyword arguments
             keyword arguments to be passed to the construction of fig and
-            axes objects of matplotlib (plt.subplots(**kwargs)).
+            axes objects of matplotlib (``plt.subplots(**kwargs)``).
             Do not use nrows or ncols arguments, since the plot grid is already
             defined by PharmaPy
 

PharmaPy/Extractors.py

@@ -11,7 +11,6 @@
 from PharmaPy.Commons import mid_fn
 from PharmaPy.Phases import LiquidPhase
 from PharmaPy.Streams import LiquidStream
-from PharmaPy.Connections import get_inputs_new
 
 from PharmaPy.Results import DynamicResult
 

PharmaPy/Interpolation.py

@@ -8,7 +8,6 @@
 
 import numpy as np
 import matplotlib.pyplot as plt
-from scipy.interpolate import CubicSpline
 from scipy.special import comb
 
 

PharmaPy/Kinetics.py

@@ -125,14 +125,17 @@ class RxnKinetics:
     r"""
     Create a reaction kinetics object. Reaction rate r\ :sub:`i` is assumed to
     have the following functional form:
-        r\ :sub:`i` = f\ :sub:`1` (T) * f\ :sub:`2` ( C\ :sub:`1`, ..., C\ :sub:`n_comp`)
+
+    r\ :sub:`i` = f\ :sub:`1` (T) * f\ :sub:`2` ( C\ :sub:`1`, ..., C\ :sub:`n_comp`)
 
     with the temperature-dependent term f\ :sub:`1` given by:
-        f\ :sub:`1` = k\ :sub:`i` * exp(- Ea\ :sub:`i`/R/T)
+
+    f\ :sub:`1` = k\ :sub:`i` * exp(- Ea\ :sub:`i`/R/T)
 
     Composition-dependent term f\ :sub:`2` can be passed as a user-defined
     function. If not given, f\ :sub:`2` is assumed to be of the form:
-        f\ :sub:`2` = prod\ :sub:`j in reactants for rxn i` C\ :sub:`j` (alpha\ :sub:`{i,j}`)
+
+    f\ :sub:`2` = prod\ :sub:`j in reactants for rxn i` C\ :sub:`j` (alpha\ :sub:`{i,j}`)
 
     where alpha\ :sub:`{i,j}` values are determined automatically by PharmaPy from
     the stoichiometric matrix of the reaction system. Custom reaction
@@ -167,6 +170,7 @@ class RxnKinetics:
         pure-component json file. If 'rxn_list' is None, then both
         stoichiometric_matrix' and 'partic_species' have to be passed
         (see below). The default is None.
+
     stoiciometric_matrix : numpy array, optional
         stoichiometric matrix for the set of reactions. It must have
         n_rxn rows and n_comp columns, so the element (i, j) represents