removed idea editor files and added gitignore

updated CI python versions, increased version number to 1.1

fixed matplotlib private method removed, removed outdated README in tests folder

pre-commit run --all-files

removed np.array on ckeys

addressed ci message:

    Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v1. Please update your workflow to use either v3 or v4

.github/workflows/ci.yml

@@ -9,21 +9,21 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v1
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
         restore-keys:
           pip-pre-commit-
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Install python dependencies
       run:
@@ -39,23 +39,23 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v1
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
         restore-keys:
           pip-pre-commit-
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/publish.yml

@@ -18,10 +18,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - run: python .github/workflows/check_release_tag.py $GITHUB_REF setup.json
 
   pre-commit:
@@ -41,10 +41,10 @@ jobs:
         restore-keys:
           pip-pre-commit-
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Install python dependencies
       run:
@@ -60,7 +60,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
     - name: Checkout
@@ -100,10 +100,10 @@ jobs:
     steps:
     - name: Checkout source
       uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Build package
       run: |
         pip install wheel

.gitignore

@@ -50,6 +50,9 @@ coverage.xml
 # Visual Studio Code
 .vscode/
 
+# idea editor
+.idea
+
 # Translations
 *.mo
 *.pot

setup.json

@@ -1,21 +1,21 @@
 {
     "name": "sportran",
-    "version": "1.0.0rc4",
+    "version": "1.1.0",
     "author": "Loris Ercole, Riccardo Bertossa, Sebastiano Bisacchi",
     "author_email": "[email protected]",
     "description": "Cepstral Data Analysis of current time series for Green-Kubo transport coefficients",
     "license": "GPL 3",
     "url": "https://github.com/sissaschool/sportran",
     "keywords": "cepstral data analysis thermal conductivity transport coefficients physics green-kubo",
-    "python_requires": ">=3.7, <4",
+    "python_requires": ">=3.9, <4",
     "classifiers": [
         "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
         "Operating System :: OS Independent",
         "Intended Audience :: Science/Research",

sportran/i_o/read_lammps_dump.py

@@ -144,7 +144,7 @@ def _read_ckeys(self, group_vectors=True, preload_timesteps=True):
             line = self.file.readline()
             if len(line) == 0:   # EOF
                 raise RuntimeError('Reached EOF, no ckeys found.')
-            values = np.array(line.split())
+            values = line.split()
             if (values[0] == 'ITEM:'):
                 if (values[1] == 'TIMESTEP'):
                     self.current_timestep = int(self.file.readline())

sportran/i_o/read_lammps_log.py

@@ -231,7 +231,7 @@ def _read_ckeys(self, run_keyword, group_vectors=True):
             nlines += 1
             if len(line) == 0:   # EOF
                 raise RuntimeError('Reached EOF, no ckeys found.')
-            values = np.array(line.split())
+            values = line.split()
             # find the column headers line
             if (len(values) and (is_string(values[0])) and (values[0] == 'Step')):
                 log.write_log('  column headers found at line {:d}. Reading data...'.format(nlines))

sportran/i_o/read_tablefile.py

@@ -191,7 +191,7 @@ def _read_ckeys(self, group_vectors=True):
             line = self.file.readline()
             if len(line) == 0:   # EOF
                 raise RuntimeError('Reached EOF, no ckeys found.')
-            values = np.array(line.split())
+            values = line.split()
             # text line: read variables names and save indexes in ckey
             if (is_string(values[0]) and (values[0].find('#') < 0)):
                 self.header += line[:-1]

sportran/plotter/plotter.py

@@ -144,10 +144,8 @@ def plot_cospectrum_component(current, idx1, idx2, *, axis=None, FIGSIZE=None, f
     """
     if axis is None:
         figure, axis = plt.subplots(1, figsize=FIGSIZE)
-    color1 = next(iter_colors)
-    color2 = next(iter_colors)
-    axis.plot(current.freqs_THz, np.real(current.fcospectrum[idx1][idx2]) * current.KAPPA_SCALE * 0.5, c=color1,)
-    axis.plot(current.freqs_THz, np.imag(current.fcospectrum[idx1][idx2]) * current.KAPPA_SCALE * 0.5, c=color2,)
+    axis.plot(current.freqs_THz, np.real(current.fcospectrum[idx1][idx2]) * current.KAPPA_SCALE * 0.5)
+    axis.plot(current.freqs_THz, np.imag(current.fcospectrum[idx1][idx2]) * current.KAPPA_SCALE * 0.5)
 
     if f_THz_max is None:
         f_THz_max = current.freqs_THz[_index_cumsum(np.abs(current.fcospectrum[idx1][idx2]), 0.95)]
@@ -192,8 +190,8 @@ def plot_ck(current, *, axis=None, label=None, FIGSIZE=None):
 
     if axis is None:
         figure, axis = plt.subplots(1, figsize=FIGSIZE)
-    color = next(iter_colors)
-    axis.plot(current.cepf.logpsdK, 'o-', c=color, label=label)
+    l, = axis.plot(current.cepf.logpsdK, 'o-', label=label)
+    color = l.get_color()
 
     axis.plot(current.cepf.logpsdK + current.cepf.logpsdK_THEORY_std, '--', c=color)
     axis.plot(current.cepf.logpsdK - current.cepf.logpsdK_THEORY_std, '--', c=color)
@@ -216,10 +214,10 @@ def plot_L0_Pstar(current, *, axis=None, label=None, FIGSIZE=None):
     """
     if axis is None:
         figure, axis = plt.subplots(1, figsize=FIGSIZE)
-    color = next(iter_colors)   # quick fix to avoid error with mlp>=3.8
-    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau, '.-', c=color, label=label)
-    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau + current.cepf.logtau_THEORY_std, '--', c=color,)
-    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau - current.cepf.logtau_THEORY_std, '--', c=color,)
+    l, = axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau, '.-', label=label)
+    color = l.get_color()
+    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau + current.cepf.logtau_THEORY_std, '--', c=color)
+    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.logtau - current.cepf.logtau_THEORY_std, '--', c=color)
     axis.axvline(x=current.cepf.aic_Kmin + 1, ls=':', c=color)
     axis.axvline(x=current.cepf.cutoffK + 1, ls='--', c=color)
     axis.set_xlim([0, 3 * current.cepf.cutoffK])
@@ -246,12 +244,11 @@ def plot_kappa_Pstar(current, *, axis=None, label=None, FIGSIZE=None, pstar_max=
     """
     if axis is None:
         figure, axis = plt.subplots(1, figsize=FIGSIZE)
-    color = next(iter_colors)
+    l, = axis.plot(np.arange(current.NFREQS) + 1, current.cepf.tau * current.KAPPA_SCALE * 0.5, 'o-', label=label)
+    color = l.get_color()
     axis.fill_between(
         np.arange(current.NFREQS) + 1, (current.cepf.tau - current.cepf.tau_THEORY_std) * current.KAPPA_SCALE * 0.5,
-        (current.cepf.tau + current.cepf.tau_THEORY_std) * current.KAPPA_SCALE * 0.5, alpha=0.3, color=color,
-    )
-    axis.plot(np.arange(current.NFREQS) + 1, current.cepf.tau * current.KAPPA_SCALE * 0.5, 'o-', c=color, label=label,)
+        (current.cepf.tau + current.cepf.tau_THEORY_std) * current.KAPPA_SCALE * 0.5, alpha=0.3, color=color)
     axis.axvline(x=current.cepf.aic_Kmin + 1, ls=':', c=color)
     axis.axvline(x=current.cepf.cutoffK + 1, ls='--', c=color)
     axis.axhline(y=current.kappa, ls='--', c=color)