Create CI/CD pipeline; various config/style updates

* Create python-package.yml

* Move dependencies to requirements.txt

* Install library; add py 3.6 & 3.7

* Update flake8 command

* Only run flake8 within ./PySeismoSoil

* Fix style in all .py files

* Fix over-indenting issue

* Stop ignoring E117

* Fix invalid escape sequence in string

* Update linting bash script

* Add testing bash script

* Add contributing instructions

* Small tweaks in style

* Add python-publish.yml

* Update doc & readme

* Update code styles in examples; fix some code

* Update sed command per https://stackoverflow.com/a/19457213

* v0.4.1 -> v0.4.2

* Move unit test folder to root folder

Author: jsh9

.github/workflows/python-package.yml

@@ -0,0 +1,38 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
+    - name: Lint with flake8
+      run: |
+        flake8 ./PySeismoSoil --count --statistics --ignore=C901,E203,E741,E221,W605,E502,E116,W504,E266,E114,E222 --max-line-length=99 --max-complexity=10
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

CONTRIBUTING.md

@@ -0,0 +1,10 @@
+# Contributing Instructions
+
+- In general, contributors should make code changes on a branch, and then [create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) to have the changes merged
+- It is strongly recommended that contributors work on code changes in an isolated Python environment
+    + Use `pip install -e .` to install this library locally, so that any local code changes are reflected immediately in your current Python environment
+- To make sure your code style is compliant, run `./run_linting.sh` locally on your computer to check style violations
+    + You might want to run `chmod +x run_linting.sh` to make `run_linting.sh` executable
+- Please also run all unit tests by running `./run_tests.sh` before committing code to GitHub
+    + You might want to run `chmod +x run_tests.sh` to make `run_tests.sh` executable
+- Even if you don't run unit tests and check code styles locally, unit tests and code styles are checked on every push at GitHub

PySeismoSoil/__init__.py

@@ -1,3 +1,3 @@
 # Author: Jian Shi
 
-__version__ = 'v0.4.1'
+__version__ = 'v0.4.2'

PySeismoSoil/class_Vs_profile.py

@@ -6,6 +6,7 @@
 
 from .class_frequency_spectrum import Frequency_Spectrum
 
+
 class Vs_Profile:
     """
     Class implementation of a Vs profile
@@ -100,9 +101,9 @@ def __init__(
         if n_col == 2:
             xi, rho = sr.get_xi_rho(vs, formula_type=xi_rho_formula)
             if thk[-1] == 0:  # last layer is an "infinity" layer
-                material_number = np.append(np.arange(1, n_layer_tmp),[0])
+                material_number = np.append(np.arange(1, n_layer_tmp), [0])
             else:
-                material_number = np.arange(1, n_layer_tmp+1)
+                material_number = np.arange(1, n_layer_tmp + 1)
             full_data = np.column_stack((thk, vs, xi, rho, material_number))
         elif n_col == 5:
             xi  = data_[:, 2]
@@ -169,7 +170,7 @@ def __repr__(self):
         for j in range(n_layer_all):
             text += '{:^10}|'.format('%.2f' % self.vs_profile[j, 0])
             text += '{:^10}|'.format('%.1f' % self.vs_profile[j, 1])
-            text += '{:^13}|'.format('%.3f' % (self.vs_profile[j, 2]*100.0))
+            text += '{:^13}|'.format('%.3f' % (self.vs_profile[j, 2] * 100.0))
             text += '{:^18}|'.format('%.1f' % self.vs_profile[j, 3])
             text += '{:^14}'.format('%d' % self.vs_profile[j, 4])
             text += '\n'

PySeismoSoil/class_frequency_spectrum.py

@@ -162,9 +162,12 @@ def plot(
         ax.set_xlabel('Frequency [Hz]')
         ax.set_ylabel('Amplitude or phase')
         ax.grid(ls=':')
-        if logx: ax.set_xscale('log')
-        if logy: ax.set_yscale('log')
-        if self._file_name: ax.set_title(self._file_name)
+        if logx:
+            ax.set_xscale('log')
+        if logy:
+            ax.set_yscale('log')
+        if self._file_name:
+            ax.set_title(self._file_name)
 
         return fig, ax
 

PySeismoSoil/class_ground_motion.py

@@ -9,6 +9,7 @@
 from PySeismoSoil.class_frequency_spectrum import Frequency_Spectrum as FS
 from PySeismoSoil.class_Vs_profile import Vs_Profile
 
+
 class Ground_Motion:
     """
     Class implementation of an earthquake ground motion.
@@ -114,7 +115,7 @@ def __init__(
 
         self.dt = float(dt)  # float; unit: sec
         self.npts = len(data_[:, 0])  # int; how many time points
-        self.time = np.linspace(0, self.dt*(self.npts-1), num=self.npts)
+        self.time = np.linspace(0, self.dt * (self.npts - 1), num=self.npts)
 
         if motion_type == 'accel':
             self.accel = data_  # numpy array, with length unit 'm'
@@ -235,7 +236,7 @@ def get_response_spectra(
         )
         return rs
 
-    def plot(self, show_as_unit='m', fig=None, ax=None, figsize=(5,6), dpi=100):
+    def plot(self, show_as_unit='m', fig=None, ax=None, figsize=(5, 6), dpi=100):
         """
         Plots acceleration, velocity, and displacement waveforms together.
 
@@ -382,13 +383,13 @@ def __calc_Arias(self, motion='accel', show_fig=False):
         Ia_1col = np.zeros(n)
         a_sq = a ** 2.0
 
-        for i in range(1,n):
+        for i in range(1, n):
             Ia_1col[i] = Ia_1col[i - 1] + np.pi / (2 * g) * a_sq[i - 1] * dt
 
         Ia_peak = float(Ia_1col[-1])
-        Ia = np.column_stack((t,Ia_1col))
+        Ia = np.column_stack((t, Ia_1col))
         Ia_norm_1col = Ia_1col / Ia_peak  # normalized
-        Ia_norm = np.column_stack((t,Ia_norm_1col))
+        Ia_norm = np.column_stack((t, Ia_norm_1col))
 
         t_low, t_high = self.__arias_time_bounds(t, Ia_norm_1col, 0.05, 0.95)
         T5_95 = t_high - t_low
@@ -426,7 +427,7 @@ def scale_motion(self, factor=1.0, target_PGA_in_g=None):
         scaled_motion : Ground_Motion
             The scaled motion
         """
-        if target_PGA_in_g != None:
+        if target_PGA_in_g is not None:
             factor = target_PGA_in_g / self.pga_in_g
         else:  # factor != None, and target_PGA_in_g is None
             pass
@@ -495,34 +496,36 @@ def truncate(self, limit, arias=True, extend=[0, 0], show_fig=False):
         n1 = int(t1 / self.dt)
         n2 = int(t2 / self.dt)
 
-        if n1 < 0: n1 = 0
-        if n2 > self.npts: n2 = self.npts
+        if n1 < 0:
+            n1 = 0
+        if n2 > self.npts:
+            n2 = self.npts
 
-        time_trunc = self.accel[:n2-n1, 0]
+        time_trunc = self.accel[:n2 - n1, 0]
         accel_trunc = self.accel[n1:n2, 1]
         truncated = np.column_stack((time_trunc, accel_trunc))
 
         if show_fig:
             ax = [None] * 3
-            fig = plt.figure(figsize=(5,6))
+            fig = plt.figure(figsize=(5, 6))
             fig.subplots_adjust(left=0.2)
 
-            ax[0] = fig.add_subplot(3,1,1)
-            ax[0].plot(self.time, self.accel[:,1], 'gray', lw=1.75, label='original')
-            ax[0].plot(self.time[n1:n2], truncated[:,1], 'm', lw=1., label='truncated')
+            ax[0] = fig.add_subplot(3, 1, 1)
+            ax[0].plot(self.time, self.accel[:, 1], 'gray', lw=1.75, label='original')
+            ax[0].plot(self.time[n1:n2], truncated[:, 1], 'm', lw=1., label='truncated')
             ax[0].grid(ls=':')
             ax[0].set_ylabel('Accel. [m/s/s]')
             ax[0].legend(loc='best')
 
-            ax[1] = fig.add_subplot(3,1,2)
-            ax[1].plot(self.time, self.veloc[:,1], 'gray', lw=1.75)
-            ax[1].plot(self.time[n1:n2], sr.num_int(truncated)[0][:,1], 'm', lw=1.)
+            ax[1] = fig.add_subplot(3, 1, 2)
+            ax[1].plot(self.time, self.veloc[:, 1], 'gray', lw=1.75)
+            ax[1].plot(self.time[n1:n2], sr.num_int(truncated)[0][:, 1], 'm', lw=1.)
             ax[1].grid(ls=':')
             ax[1].set_ylabel('Veloc. [m/s]')
 
-            ax[2] = fig.add_subplot(3,1,3)
-            ax[2].plot(self.time, self.displ[:,1], 'gray', lw=1.75)
-            ax[2].plot(self.time[n1:n2], sr.num_int(truncated)[1][:,1], 'm', lw=1.)
+            ax[2] = fig.add_subplot(3, 1, 3)
+            ax[2].plot(self.time, self.displ[:, 1], 'gray', lw=1.75)
+            ax[2].plot(self.time[n1:n2], sr.num_int(truncated)[1][:, 1], 'm', lw=1.)
             ax[2].grid(ls=':')
             ax[2].set_ylabel('Displ. [m]')
             ax[2].set_xlabel('Time [sec]')
@@ -882,8 +885,8 @@ def save_accel(
         if unit == 'm/s/s':
             pass
         elif unit == 'g':
-            data[:,1] = data[:,1] / 9.81
+            data[:, 1] = data[:, 1] / 9.81
         elif unit in ['gal', 'cm/s/s']:
-            data[:,1] = data[:,1] * 100.0
+            data[:, 1] = data[:, 1] * 100.0
 
         np.savetxt(fname, data, fmt=fmt, delimiter=sep)

PySeismoSoil/class_hh_calibration.py

@@ -5,6 +5,7 @@
 from . import helper_generic as hlp
 from . import helper_hh_calibration as hhc
 
+
 class HH_Calibration:
     """
     Class implementation of the "HH calibration procedure" (HHC procedure). The
@@ -68,7 +69,8 @@ def __init__(self, vs_profile, *, GGmax_curves=None, Tmax_profile=None):
         self.GGmax_curves = GGmax_curves
         self.Tmax_profile = Tmax_profile
 
-    def fit(self, show_fig=False, save_fig=False, fig_output_dir=None,
+    def fit(
+            self, show_fig=False, save_fig=False, fig_output_dir=None,
             save_HH_G_file=False, HH_G_file_dir=None, profile_name=None,
             verbose=True,
     ):

PySeismoSoil/class_parameters.py

@@ -142,7 +142,7 @@ def get_damping(self, strain_in_pct=np.logspace(-2, 1)):
             print('You did not provide a function to calculate shear stress.')
             return None
         damping_in_1 = sr.calc_damping_from_param(
-            self.data, strain_in_pct/100., self.func_stress,
+            self.data, strain_in_pct / 100., self.func_stress,
         )
         return damping_in_1 * 100
 

PySeismoSoil/class_simulation.py

@@ -107,7 +107,8 @@ class Linear_Simulation(Simulation):
     ----------
     Attributes same as the inputs
     """
-    def run(self, every_layer=True, deconv=False, show_fig=False,
+    def run(
+            self, every_layer=True, deconv=False, show_fig=False,
             save_fig=False, motion_name=None, save_txt=False,
             save_full_time_history=False, output_dir=None, verbose=True,
     ):
@@ -168,7 +169,7 @@ def run(self, every_layer=True, deconv=False, show_fig=False,
                 Vs_Profile(new_profile, density_unit='g/cm^3'),
                 max_a_v_d=max_avd,
                 max_strain_stress=max_gt,
-                trans_func=Frequency_Spectrum(tf, df=freq_array[1]-freq_array[0]),
+                trans_func=Frequency_Spectrum(tf, df=freq_array[1] - freq_array[0]),
                 time_history_accel=out_a,
                 time_history_veloc=out_v,
                 time_history_displ=out_d,
@@ -239,7 +240,8 @@ def __init__(
             soil_profile, GGmax_and_damping_curves=GGmax_and_damping_curves,
         )
 
-    def run(self, verbose=True, show_fig=False, save_fig=False,
+    def run(
+            self, verbose=True, show_fig=False, save_fig=False,
             motion_name=None, save_txt=False, save_full_time_history=False,
             output_dir=None,
     ):
@@ -293,7 +295,7 @@ def run(self, verbose=True, show_fig=False, save_fig=False,
             Vs_Profile(new_profile, density_unit='g/cm^3'),
             max_a_v_d=max_avd,
             max_strain_stress=max_gt,
-            trans_func=Frequency_Spectrum(tf, df=freq_array[1]-freq_array[0]),
+            trans_func=Frequency_Spectrum(tf, df=freq_array[1] - freq_array[0]),
             time_history_accel=out_a,
             time_history_veloc=out_v,
             time_history_displ=out_d,
@@ -351,7 +353,8 @@ def __init__(
         )
         sim.check_layer_count(soil_profile, G_param=G_param, xi_param=xi_param)
 
-    def run(self, sim_dir=None, motion_name=None, save_txt=False,
+    def run(
+            self, sim_dir=None, motion_name=None, save_txt=False,
             save_full_time_history=True, show_fig=False, save_fig=False,
             remove_sim_dir=False, verbose=True,
     ):
@@ -434,7 +437,7 @@ def run(self, sim_dir=None, motion_name=None, save_txt=False,
             [1.32629E+01, -1.33696E-01, 2.14647E-01],
         ])
 
-        #--------- Re-discretize Vs profile -----------------------------------
+        # --------- Re-discretize Vs profile -----------------------------------
         new_profile = sr.stratify(self.soil_profile.vs_profile)
         new_profile[:, 3] /= 1000.0  # convert to g/cm3 to pass to NLHH
 
@@ -448,12 +451,12 @@ def run(self, sim_dir=None, motion_name=None, save_txt=False,
         t = input_accel[:, 0]
         nt_out = len(t)
 
-        #--------- Create a dummy "curves" for Fortran ------------------------
+        # --------- Create a dummy "curves" for Fortran ------------------------
         mgc, mdc = self.G_param.construct_curves(strain_in_pct=strain_in_pct)
         mgdc = Multiple_GGmax_Damping_Curves(mgc_and_mdc=(mgc, mdc))
         curves = mgdc.get_curve_matrix()
 
-        #--------- Prepare tabk.dat file --------------------------------------
+        # --------- Prepare tabk.dat file --------------------------------------
         if hlp.detect_OS() == 'Windows':
             exec_ext = 'exe'
         elif hlp.detect_OS() == 'Darwin':
@@ -468,21 +471,21 @@ def run(self, sim_dir=None, motion_name=None, save_txt=False,
         shutil.copy(os.path.join(dir_exec_files, 'NLHH.%s' % exec_ext), sim_dir)
         np.savetxt(os.path.join(sim_dir, 'tabk.dat'), tabk, delimiter='\t')
 
-        #-------- Prepare control.dat file ------------------------------------
+        # -------- Prepare control.dat file ------------------------------------
         with open(os.path.join(sim_dir, 'control.dat'), 'w') as fp:
             fp.write(
                 '%6.1f %6.0f %6.0f %6.0f %6.0f %10.0f %6.0f %6.0f %6.0f' \
                 % (f_max, ppw, n_dt, n_bound, n_layer, nt_out, n_ma, N_spr, N_obs)
             )
 
-        #-------- Write data to files for the Fortran kernel to read ----------
+        # -------- Write data to files for the Fortran kernel to read ----------
         np.savetxt(os.path.join(sim_dir, 'profile.dat'), new_profile)
         np.savetxt(os.path.join(sim_dir, 'incident.dat'), input_accel)
         np.savetxt(os.path.join(sim_dir, 'curve.dat'), curves)
         np.savetxt(os.path.join(sim_dir, 'HH_G.dat'), self.G_param.serialize_to_2D_array())
         np.savetxt(os.path.join(sim_dir, 'HH_x.dat'), self.xi_param.serialize_to_2D_array())
 
-        #------- Execute Fortran kernel ---------------------------------------
+        # ------- Execute Fortran kernel ---------------------------------------
         cwd = os.getcwd()
         os.chdir(sim_dir)
         if hlp.detect_OS() == 'Windows':
@@ -507,7 +510,7 @@ def run(self, sim_dir=None, motion_name=None, save_txt=False,
         if verbose:
             print('Simulation finished. Now post processing.')
 
-        #------------ Post-process files --------------------------------------
+        # ------------ Post-process files --------------------------------------
         layer_boundary_depth = np.genfromtxt('node_depth.dat').T
         layer_midpoint_depth = np.genfromtxt('layer_depth.dat').T
         out_a = np.genfromtxt('out_a.dat')
@@ -549,7 +552,7 @@ def run(self, sim_dir=None, motion_name=None, save_txt=False,
         )
         os.chdir(cwd)
 
-        #------------ Create sim_results object and plot and/or save ----------
+        # ------------ Create sim_results object and plot and/or save ----------
         sim_results = Simulation_Results(
             self.input_motion,
             Ground_Motion(accel_surface_2col, unit='m'),