From 0d597d7a70f52f88191ea6ae2fef7ef03c245256 Mon Sep 17 00:00:00 2001 From: Mark Bouman <103944120+markbouman@users.noreply.github.com> Date: Sun, 6 Nov 2022 22:12:46 -0500 Subject: [PATCH 01/23] Bug fixes (#229) --- impedance/models/circuits/circuits.py | 2 +- impedance/validation.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/impedance/models/circuits/circuits.py b/impedance/models/circuits/circuits.py index 818be2fb..630a9d9b 100644 --- a/impedance/models/circuits/circuits.py +++ b/impedance/models/circuits/circuits.py @@ -28,7 +28,7 @@ def __init__(self, initial_guess=[], constants=None, name=None): """ # if supplied, check that initial_guess is valid and store - initial_guess = list(filter(None, initial_guess)) + initial_guess = [x for x in initial_guess if x is not None] for i in initial_guess: if not isinstance(i, (float, int, np.int32, np.float64)): raise TypeError(f'value {i} in initial_guess is not a number') diff --git a/impedance/validation.py b/impedance/validation.py index fa00f90a..6e9a2a84 100644 --- a/impedance/validation.py +++ b/impedance/validation.py @@ -91,7 +91,7 @@ def linKK(f, Z, c=0.85, max_M=50, fit_type='real', add_cap=False): if c is not None: M = 0 mu = 1 - while mu > c and M <= max_M: + while mu > c and M < max_M: M += 1 ts = get_tc_distribution(f, M) elements, mu = fit_linKK(f, ts, M, Z, fit_type, add_cap) From 364b789f49d9dfce8ffc03baa2d616063a30e98c Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sun, 6 Nov 2022 19:21:53 -0800 Subject: [PATCH 02/23] docs: add markbouman as a contributor for bug, and code (#230) --- .all-contributorsrc | 13 ++++++++++++- README.md | 37 +++++++++++++++++++------------------ 2 files changed, 31 insertions(+), 19 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index f5bcbb8d..6d66cf66 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -181,6 +181,16 @@ "contributions": [ "bug" ] + }, + { + "login": "markbouman", + "name": "Mark Bouman", + "avatar_url": "https://avatars.githubusercontent.com/u/103944120?v=4", + "profile": "https://github.com/markbouman", + "contributions": [ + "bug", + "code" + ] } ], "contributorsPerLine": 7, @@ -188,5 +198,6 @@ "projectOwner": "ECSHackWeek", "repoType": "github", "repoHost": "https://github.com", - "skipCi": true + "skipCi": true, + "commitConvention": "angular" } diff --git a/README.md b/README.md index 96c30f74..607101c1 100644 --- a/README.md +++ b/README.md @@ -72,28 +72,29 @@ This project started at the [2018 Electrochemical Society (ECS) Hack Week in Sea - - - - - - - + + + + + + + - - - - - - - + + + + + + + - - - - + + + + +

Lok-kun Tsui
💻 ⚠️ 📖
Brian Gerwe
💻 ⚠️ 📖 👀
Neal
👀 💻
Matt Murbach
📖 👀 ⚠️ 💻
Kenny Huynh
🐛 💻
lawrencerenna
🤔
Rowin
🐛 💻		Lok-kun Tsui
Lok-kun Tsui
💻 ⚠️ 📖		Brian Gerwe
Brian Gerwe
💻 ⚠️ 📖 👀		Neal
Neal
👀 💻		Matt Murbach
Matt Murbach
📖 👀 ⚠️ 💻		Kenny Huynh
Kenny Huynh
🐛 💻		lawrencerenna
lawrencerenna
🤔		Rowin
Rowin
🐛 💻

Michael Plews
🤔
Chebuskin
🐛
environmat
🐛
Abdullah Sumbal
🐛
nobkat
💻
Nick
🐛 💻
aokomorowski
💻		Michael Plews
Michael Plews
🤔		Chebuskin
Chebuskin
🐛		environmat
environmat
🐛		Abdullah Sumbal
Abdullah Sumbal
🐛		nobkat
nobkat
💻		Nick
Nick
🐛 💻		aokomorowski
aokomorowski
💻

Peter Attia
💻 ⚠️ 📖
sdkang
⚠️ 💻
lucasfdvx
🐛
Marcus Karlstad
🐛		Peter Attia
Peter Attia
💻 ⚠️ 📖		sdkang
sdkang
⚠️ 💻		lucasfdvx
lucasfdvx
🐛		Marcus Karlstad
Marcus Karlstad
🐛		Mark Bouman
Mark Bouman
🐛 💻
From 7384f0a51e21cc5c3951c99278ad1f0d5c881807 Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 12:30:00 -0800 Subject: [PATCH 03/23] bump version to 1.4.2 --- impedance/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/impedance/__init__.py b/impedance/__init__.py index bf256159..daa50c7c 100644 --- a/impedance/__init__.py +++ b/impedance/__init__.py @@ -1 +1 @@ -__version__ = "1.4.1" +__version__ = "1.4.2" From 9dbca0928c84b0e8750ff686ea1cf7f4f6b29637 Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 13:09:16 -0800 Subject: [PATCH 04/23] Removes Python 3.6 from test matrix (#240) * removes Python 3.6 from test matrix as it has reached EOL and is no longer supported by ubuntu-latest runners * remove support for Python 3.6 * replace np.complex with built-in complex --- .github/workflows/ci.yml | 14 +++++++------- README.md | 2 +- impedance/tests/test_circuits.py | 2 +- setup.py | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b34bf2f..54b5f766 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,12 +11,12 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2.3.4 + - uses: actions/checkout@v3 - name: Set up Python 3.6 - uses: actions/setup-python@v2.2.2 + uses: actions/setup-python@v3 with: - python-version: 3.6 + python-version: 3.7 - name: Install dependencies run: | @@ -37,13 +37,13 @@ jobs: fail-fast: false max-parallel: 4 matrix: - python-version: [3.6, 3.7, 3.8, 3.9] + python-version: [3.7, 3.8, 3.9, 3.10, 3.11] steps: - - uses: actions/checkout@v2.3.4 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2.2.2 + uses: actions/setup-python@v3 with: python-version: ${{ matrix.python_version }} @@ -58,7 +58,7 @@ jobs: pytest --cov=impedance . - name: Upload coverage to coveralls - if: matrix.python-version == 3.6 && github.repository == 'ECSHackWeek/impedance.py' + if: matrix.python-version == 3.7 && github.repository == 'ECSHackWeek/impedance.py' run: coveralls --service=github env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/README.md b/README.md index 607101c1..dcfc4264 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ See [Getting started with impedance.py](https://impedancepy.readthedocs.io/en/la impedance.py requires: -- Python (>=3.6) +- Python (>=3.7) - SciPy (>=1.0) - NumPy (>=1.14) - Matplotlib (>=3.0) diff --git a/impedance/tests/test_circuits.py b/impedance/tests/test_circuits.py index 9664aebd..088e5776 100644 --- a/impedance/tests/test_circuits.py +++ b/impedance/tests/test_circuits.py @@ -72,7 +72,7 @@ def test_Randles(): # compare with known impedance predictions assert np.isclose(randles.predict(np.array([10.0])), - np.complex(0.0251618, -0.00601304)) + complex(0.0251618, -0.00601304)) # check altair plotting with a fit circuit chart = randles.plot(f_data=f, Z_data=Z) diff --git a/setup.py b/setup.py index 9ef25aa4..dd77f136 100644 --- a/setup.py +++ b/setup.py @@ -14,7 +14,7 @@ long_description_content_type="text/markdown", url="https://impedancepy.readthedocs.io/en/latest/", packages=setuptools.find_packages(), - python_requires="~=3.6", + python_requires="~=3.7", install_requires=['altair>=3.0', 'matplotlib>=3.0', 'numpy>=1.14', 'scipy>=1.0'], classifiers=( From b1838632b1f00e1ea933be952a1a40e28ea56f0c Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 13:51:34 -0800 Subject: [PATCH 05/23] add build and push to pypi in ci workflow (#241) * add build and push to pypi in ci workflow * install wheel package * run jobs sequentially * remove test publish to test.pypi.org/legacy --- .github/workflows/ci.yml | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 54b5f766..85a3c84e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,4 +1,4 @@ -name: CI tests +name: Run tests and build package on: pull_request: push: @@ -31,11 +31,12 @@ jobs: tests: name: Run tests + needs: linting runs-on: ubuntu-latest strategy: fail-fast: false - max-parallel: 4 + max-parallel: 5 matrix: python-version: [3.7, 3.8, 3.9, 3.10, 3.11] @@ -62,3 +63,27 @@ jobs: run: coveralls --service=github env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + build-and-push: + name: Build and publish package to PyPI + needs: [linting, tests] + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@master + + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: "3.10" + + - name: Build a binary wheel and a source tarball + run: | + python3 -m pip install wheel + python3 setup.py sdist bdist_wheel + + - name: Publish distribution to PyPI (if tagged) + if: startsWith(github.ref, 'refs/tags') + uses: pypa/gh-action-pypi-publish@release/v1 + with: + password: ${{ secrets.PYPI_API_TOKEN }} From 047e716dfd6c64b1a181a120195ef6f2c3b7fb8a Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 14:07:42 -0800 Subject: [PATCH 06/23] add tags to github workflow --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 85a3c84e..f00db9e4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,6 +4,8 @@ on: push: branches: - main + tags: + - * jobs: linting: From 2b53caf7500624756cdc48476a57adf33f3ffbf1 Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 14:07:42 -0800 Subject: [PATCH 07/23] add tags to github workflow --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 85a3c84e..5c01c814 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,6 +4,8 @@ on: push: branches: - main + tags: + - '*' jobs: linting: From 41d00fbdb053beeb8ad9b06113b24668a94fa48c Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sat, 28 Jan 2023 14:25:59 -0800 Subject: [PATCH 08/23] docs: add oslopanda as a contributor for bug (#242) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> --- .all-contributorsrc | 9 +++++++++ README.md | 39 ++++++++++++++++++++------------------- 2 files changed, 29 insertions(+), 19 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 6d66cf66..4af194c6 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -191,6 +191,15 @@ "bug", "code" ] + }, + { + "login": "oslopanda", + "name": "oslopanda", + "avatar_url": "https://avatars.githubusercontent.com/u/33810430?v=4", + "profile": "https://github.com/oslopanda", + "contributions": [ + "bug" + ] } ], "contributorsPerLine": 7, diff --git a/README.md b/README.md index dcfc4264..91c8b0aa 100644 --- a/README.md +++ b/README.md @@ -72,29 +72,30 @@ This project started at the [2018 Electrochemical Society (ECS) Hack Week in Sea - - - - - - - + + + + + + + - - - - - - - + + + + + + + - - - - - + + + + + +
Lok-kun Tsui
Lok-kun Tsui
💻 ⚠️ 📖		Brian Gerwe
Brian Gerwe
💻 ⚠️ 📖 👀		Neal
Neal
👀 💻		Matt Murbach
Matt Murbach
📖 👀 ⚠️ 💻		Kenny Huynh
Kenny Huynh
🐛 💻		lawrencerenna
lawrencerenna
🤔		Rowin
Rowin
🐛 💻		Lok-kun Tsui
Lok-kun Tsui
💻 ⚠️ 📖		Brian Gerwe
Brian Gerwe
💻 ⚠️ 📖 👀		Neal
Neal
👀 💻		Matt Murbach
Matt Murbach
📖 👀 ⚠️ 💻		Kenny Huynh
Kenny Huynh
🐛 💻		lawrencerenna
lawrencerenna
🤔		Rowin
Rowin
🐛 💻
Michael Plews
Michael Plews
🤔		Chebuskin
Chebuskin
🐛		environmat
environmat
🐛		Abdullah Sumbal
Abdullah Sumbal
🐛		nobkat
nobkat
💻		Nick
Nick
🐛 💻		aokomorowski
aokomorowski
💻		Michael Plews
Michael Plews
🤔		Chebuskin
Chebuskin
🐛		environmat
environmat
🐛		Abdullah Sumbal
Abdullah Sumbal
🐛		nobkat
nobkat
💻		Nick
Nick
🐛 💻		aokomorowski
aokomorowski
💻
Peter Attia
Peter Attia
💻 ⚠️ 📖		sdkang
sdkang
⚠️ 💻		lucasfdvx
lucasfdvx
🐛		Marcus Karlstad
Marcus Karlstad
🐛		Mark Bouman
Mark Bouman
🐛 💻		Peter Attia
Peter Attia
💻 ⚠️ 📖		sdkang
sdkang
⚠️ 💻		lucasfdvx
lucasfdvx
🐛		Marcus Karlstad
Marcus Karlstad
🐛		Mark Bouman
Mark Bouman
🐛 💻		oslopanda
oslopanda
🐛
From fd2e91b95d111228da6edec90a9fb52cb6b7276e Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sat, 28 Jan 2023 14:28:01 -0800 Subject: [PATCH 09/23] docs: add pililac as a contributor for bug (#243) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> --- .all-contributorsrc | 9 +++++++++ README.md | 1 + 2 files changed, 10 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 4af194c6..dbfa5f30 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -200,6 +200,15 @@ "contributions": [ "bug" ] + }, + { + "login": "pililac", + "name": "pililac", + "avatar_url": "https://avatars.githubusercontent.com/u/60116646?v=4", + "profile": "https://github.com/pililac", + "contributions": [ + "bug" + ] } ], "contributorsPerLine": 7, diff --git a/README.md b/README.md index 91c8b0aa..fd005c85 100644 --- a/README.md +++ b/README.md @@ -96,6 +96,7 @@ This project started at the [2018 Electrochemical Society (ECS) Hack Week in Sea Marcus Karlstad
Marcus Karlstad
🐛 Mark Bouman
Mark Bouman
🐛 💻 oslopanda
oslopanda
🐛 + pililac
pililac
🐛 From 5b821d42d321bc720a629540a550c72ce970d359 Mon Sep 17 00:00:00 2001 From: Kavin Teenakul Date: Sat, 28 Jan 2023 23:29:58 +0100 Subject: [PATCH 10/23] Update preprocessing.py (#233) Fix typo --- impedance/preprocessing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/impedance/preprocessing.py b/impedance/preprocessing.py index ed96b910..1cfe55d4 100644 --- a/impedance/preprocessing.py +++ b/impedance/preprocessing.py @@ -324,7 +324,7 @@ def readZPlot(filename): def readPowerSuite(filename): - """ function for reading the .txt file from Parstat + """ function for reading the .txt file from PowerSuite Parameters ---------- From 77f3c3b2b611fb83cf01e4bd7de912e74547053a Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sat, 28 Jan 2023 14:31:38 -0800 Subject: [PATCH 11/23] docs: add kevinsmia1939 as a contributor for code (#244) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> --- .all-contributorsrc | 9 +++++++++ README.md | 3 +++ 2 files changed, 12 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index dbfa5f30..cbcf5966 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -209,6 +209,15 @@ "contributions": [ "bug" ] + }, + { + "login": "kevinsmia1939", + "name": "Kavin Teenakul", + "avatar_url": "https://avatars.githubusercontent.com/u/11407922?v=4", + "profile": "https://github.com/kevinsmia1939", + "contributions": [ + "code" + ] } ], "contributorsPerLine": 7, diff --git a/README.md b/README.md index fd005c85..9e953993 100644 --- a/README.md +++ b/README.md @@ -98,6 +98,9 @@ This project started at the [2018 Electrochemical Society (ECS) Hack Week in Sea oslopanda
oslopanda
🐛 pililac
pililac
🐛 + + Kavin Teenakul
Kavin Teenakul
💻 + From 43dbe6c0e46b52d6e1dcd6fc68b989f357bb8a82 Mon Sep 17 00:00:00 2001 From: oslopanda <33810430+oslopanda@users.noreply.github.com> Date: Sat, 28 Jan 2023 23:38:23 +0100 Subject: [PATCH 12/23] Plotting update and a bug fix (#237) * Update visualization.py * Update visualization.py * Update circuits.py * Update impedance/models/circuits/circuits.py --------- Co-authored-by: Matt Murbach --- impedance/models/circuits/circuits.py | 2 +- impedance/visualization.py | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/impedance/models/circuits/circuits.py b/impedance/models/circuits/circuits.py index 630a9d9b..c9c7f467 100644 --- a/impedance/models/circuits/circuits.py +++ b/impedance/models/circuits/circuits.py @@ -188,7 +188,7 @@ def __str__(self): for name, value in self.constants.items(): elem = get_element_from_name(name) units = check_and_eval(elem).units - if '_' in name: + if '_' in name and len(units) > 1 : unit = units[int(name.split('_')[-1])] else: unit = units[0] diff --git a/impedance/visualization.py b/impedance/visualization.py index e08568ad..ec3ce40c 100644 --- a/impedance/visualization.py +++ b/impedance/visualization.py @@ -4,7 +4,7 @@ import pandas as pd -def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, **kwargs): +def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, labelsize=20, ticksize=14, **kwargs): """ Plots impedance as a Nyquist plot using matplotlib Parameters @@ -42,12 +42,12 @@ def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, **kwargs): # Set the labels to -imaginary vs real ax.set_xlabel(r'$Z^{\prime}(\omega)$ ' + - '$[{}]$'.format(units), fontsize=20) + '$[{}]$'.format(units), fontsize=labelsize) ax.set_ylabel(r'$-Z^{\prime\prime}(\omega)$ ' + - '$[{}]$'.format(units), fontsize=20) + '$[{}]$'.format(units), fontsize=labelsize) # Make the tick labels larger - ax.tick_params(axis='both', which='major', labelsize=14) + ax.tick_params(axis='both', which='major', labelsize=ticksize) # Change the number of labels on each axis to five ax.locator_params(axis='x', nbins=5, tight=True) @@ -69,7 +69,7 @@ def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, **kwargs): return ax -def plot_bode(f, Z, scale=1, units='Ohms', fmt='.-', axes=None, **kwargs): +def plot_bode(f, Z, scale=1, units='Ohms', fmt='.-', axes=None, labelsize=20, ticksize=14, **kwargs): """ Plots impedance as a Bode plot using matplotlib Parameters @@ -109,16 +109,16 @@ def plot_bode(f, Z, scale=1, units='Ohms', fmt='.-', axes=None, **kwargs): # Set the y-axis labels ax_mag.set_ylabel(r'$|Z(\omega)|$ ' + - '$[{}]$'.format(units), fontsize=20) - ax_phs.set_ylabel(r'$-\phi_Z(\omega)$ ' + r'$[^o]$', fontsize=20) + '$[{}]$'.format(units), fontsize=labelsize) + ax_phs.set_ylabel(r'$-\phi_Z(\omega)$ ' + r'$[^o]$', fontsize=labelsize) for ax in axes: # Set the frequency axes title and make log scale - ax.set_xlabel('f [Hz]', fontsize=20) + ax.set_xlabel('f [Hz]', fontsize=labelsize) ax.set_xscale('log') # Make the tick labels larger - ax.tick_params(axis='both', which='major', labelsize=14) + ax.tick_params(axis='both', which='major', labelsize=ticksize) # Change the number of labels on each axis to five ax.locator_params(axis='y', nbins=5, tight=True) From d1315b25a551afd80b45cb1e575c0b2d2be36fb6 Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 14:40:12 -0800 Subject: [PATCH 13/23] fix inadvertant whitespace --- impedance/models/circuits/circuits.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/impedance/models/circuits/circuits.py b/impedance/models/circuits/circuits.py index c9c7f467..70d402bb 100644 --- a/impedance/models/circuits/circuits.py +++ b/impedance/models/circuits/circuits.py @@ -188,7 +188,7 @@ def __str__(self): for name, value in self.constants.items(): elem = get_element_from_name(name) units = check_and_eval(elem).units - if '_' in name and len(units) > 1 : + if '_' in name and len(units) > 1: unit = units[int(name.split('_')[-1])] else: unit = units[0] From 019f958bb4d93e0bbc1a2371b2595578d2da3804 Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 14:45:37 -0800 Subject: [PATCH 14/23] fix PEP8 long lines issues in visualization.py --- impedance/visualization.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/impedance/visualization.py b/impedance/visualization.py index ec3ce40c..4d5f9d7a 100644 --- a/impedance/visualization.py +++ b/impedance/visualization.py @@ -4,7 +4,8 @@ import pandas as pd -def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, labelsize=20, ticksize=14, **kwargs): +def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, labelsize=20, + ticksize=14, **kwargs): """ Plots impedance as a Nyquist plot using matplotlib Parameters @@ -69,7 +70,8 @@ def plot_nyquist(Z, scale=1, units='Ohms', fmt='.-', ax=None, labelsize=20, tick return ax -def plot_bode(f, Z, scale=1, units='Ohms', fmt='.-', axes=None, labelsize=20, ticksize=14, **kwargs): +def plot_bode(f, Z, scale=1, units='Ohms', fmt='.-', axes=None, labelsize=20, + ticksize=14, **kwargs): """ Plots impedance as a Bode plot using matplotlib Parameters From ecaae60f6bf20d2d87db7a18f131cf69bebbe43a Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Sat, 28 Jan 2023 14:55:31 -0800 Subject: [PATCH 15/23] bump version to v1.4.3 --- impedance/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/impedance/__init__.py b/impedance/__init__.py index daa50c7c..aa56ed40 100644 --- a/impedance/__init__.py +++ b/impedance/__init__.py @@ -1 +1 @@ -__version__ = "1.4.2" +__version__ = "1.4.3" From 059df991f4ce40d100d3280b34930aa47062531f Mon Sep 17 00:00:00 2001 From: Raymond Gasper <14928724+rgasper@users.noreply.github.com> Date: Thu, 2 Feb 2023 00:48:59 -0500 Subject: [PATCH 16/23] New Feature: Users can add their own circuit elements easily (#196) * gitignore testing output files * add ability for users to add new circuits * adjustment of overwrite circuit element behavior and test for it * make tests definitely not flaky to changes in func names * config for pylsp linter and formatter extensions to respect 80 char line limit * not allowed to name elements s or p cus it'll break everything * Update impedance/tests/test_circuit_elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/models/circuits/elements.py Co-authored-by: Matt Murbach * Update impedance/tests/test_circuit_elements.py Co-authored-by: Matt Murbach * Update impedance/tests/test_circuit_elements.py * Delete pyproject.toml * Update .gitignore * Fix Flake8 errors * Move noqa to correct lines * Remove trailing whitespace * Add test for redefining built-in functions * Fix spacing between functions --------- Co-authored-by: Matt Murbach --- .gitignore | 3 + impedance/models/circuits/elements.py | 215 ++++++++++++---------- impedance/tests/test_circuit_elements.py | 216 ++++++++++++++++++----- pylama.ini | 6 + 4 files changed, 296 insertions(+), 144 deletions(-) create mode 100644 pylama.ini diff --git a/.gitignore b/.gitignore index e3e79b56..a511eec8 100644 --- a/.gitignore +++ b/.gitignore @@ -111,3 +111,6 @@ venv.bak/ # mypy .mypy_cache/ + +# testing +*_test.csv diff --git a/impedance/models/circuits/elements.py b/impedance/models/circuits/elements.py index 26ead0b0..323159af 100644 --- a/impedance/models/circuits/elements.py +++ b/impedance/models/circuits/elements.py @@ -1,27 +1,28 @@ import numpy as np -initial_state = globals().copy() -non_element_functions = ['element_metadata', - 'initial_state', - 'non_element_functions', - 'typeChecker', - 'circuit_elements'] -# populated at the end of the file - -# this maps ex. 'R' to the function R to always give us a list of -# active elements in any context -circuit_elements = {} + +class ElementError(Exception): + ... + + +class OverwriteError(ElementError): + ... -def element_metadata(num_params, units): - """ decorator to store metadata for a circuit element +def element(num_params, units, overwrite=False): + """decorator to store metadata for a circuit element - Parameters - ---------- - num_params : int - number of parameters for an element - units : list of str - list of units for the element parameters + Parameters + ---------- + num_params : int + number of parameters for an element + units : list of str + list of units for the element parameters + overwrite : bool (default False) + if true, overwrites any existing element; if false, + raises OverwriteError if element name already exists. """ + def decorator(func): def wrapper(p, f): typeChecker(p, f, func.__name__, num_params) @@ -32,12 +33,26 @@ def wrapper(p, f): wrapper.__name__ = func.__name__ wrapper.__doc__ = func.__doc__ + global circuit_elements + if func.__name__ in ["s", "p"]: + raise ElementError("cannot redefine elements 's' (series)" + + "or 'p' (parallel)") + elif func.__name__ in circuit_elements and not overwrite: + raise OverwriteError( + f"element {func.__name__} already exists. " + + "If you want to overwrite the existing element," + + "use `overwrite=True`." + ) + else: + circuit_elements[func.__name__] = wrapper + return wrapper + return decorator def s(series): - """ sums elements in series + """sums elements in series Notes --------- @@ -45,14 +60,14 @@ def s(series): Z = Z_1 + Z_2 + ... + Z_n """ - z = len(series[0])*[0 + 0*1j] + z = len(series[0]) * [0 + 0 * 1j] for elem in series: z += elem return z def p(parallel): - """ adds elements in parallel + """adds elements in parallel Notes --------- @@ -60,16 +75,23 @@ def p(parallel): Z = \\frac{1}{\\frac{1}{Z_1} + \\frac{1}{Z_2} + ... + \\frac{1}{Z_n}} - """ - z = len(parallel[0])*[0 + 0*1j] + """ + z = len(parallel[0]) * [0 + 0 * 1j] for elem in parallel: - z += 1/elem - return 1/z + z += 1 / elem + return 1 / z -@element_metadata(num_params=1, units=['Ohm']) +# manually add parallel and series operators to circuit elements w/o metadata +# populated by the element decorator - +# this maps ex. 'R' to the function R to always give us a list of +# active elements in any context +circuit_elements = {"s": s, "p": p} + + +@element(num_params=1, units=["Ohm"]) def R(p, f): - """ defines a resistor + """defines a resistor Notes --------- @@ -79,43 +101,43 @@ def R(p, f): """ R = p[0] - Z = np.array(len(f)*[R]) + Z = np.array(len(f) * [R]) return Z -@element_metadata(num_params=1, units=['F']) +@element(num_params=1, units=["F"]) def C(p, f): - """ defines a capacitor + """defines a capacitor .. math:: Z = \\frac{1}{C \\times j 2 \\pi f} - """ - omega = 2*np.pi*np.array(f) + """ + omega = 2 * np.pi * np.array(f) C = p[0] - Z = 1.0/(C*1j*omega) + Z = 1.0 / (C * 1j * omega) return Z -@element_metadata(num_params=1, units=['H']) +@element(num_params=1, units=["H"]) def L(p, f): - """ defines an inductor + """defines an inductor .. math:: Z = L \\times j 2 \\pi f - """ - omega = 2*np.pi*np.array(f) + """ + omega = 2 * np.pi * np.array(f) L = p[0] - Z = L*1j*omega + Z = L * 1j * omega return Z -@element_metadata(num_params=1, units=['Ohm sec^-1/2']) +@element(num_params=1, units=["Ohm sec^-1/2"]) def W(p, f): - """ defines a semi-infinite Warburg element + """defines a semi-infinite Warburg element Notes ----- @@ -123,15 +145,15 @@ def W(p, f): Z = \\frac{A_W}{\\sqrt{ 2 \\pi f}} (1-j) """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) Aw = p[0] - Z = Aw*(1-1j)/np.sqrt(omega) + Z = Aw * (1 - 1j) / np.sqrt(omega) return Z -@element_metadata(num_params=2, units=['Ohm', 'sec']) +@element(num_params=2, units=["Ohm", "sec"]) def Wo(p, f): - """ defines an open (finite-space) Warburg element + """defines an open (finite-space) Warburg element Notes --------- @@ -143,15 +165,15 @@ def Wo(p, f): :math:`\\tau` = p[1] (sec) = :math:`\\frac{L^2}{D}` """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) Z0, tau = p[0], p[1] - Z = Z0/(np.sqrt(1j*omega*tau)*np.tanh(np.sqrt(1j*omega*tau))) + Z = Z0 / (np.sqrt(1j * omega * tau) * np.tanh(np.sqrt(1j * omega * tau))) return Z # Zw(omega) -@element_metadata(num_params=2, units=['Ohm', 'sec']) +@element(num_params=2, units=["Ohm", "sec"]) def Ws(p, f): - """ defines a short (finite-length) Warburg element + """defines a short (finite-length) Warburg element Notes --------- @@ -163,15 +185,15 @@ def Ws(p, f): :math:`\\tau` = p[1] (sec) = :math:`\\frac{L^2}{D}` """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) Z0, tau = p[0], p[1] - Z = Z0*np.tanh(np.sqrt(1j*omega*tau))/np.sqrt(1j*omega*tau) + Z = Z0 * np.tanh(np.sqrt(1j * omega * tau)) / np.sqrt(1j * omega * tau) return Z -@element_metadata(num_params=2, units=['Ohm^-1 sec^a', '']) +@element(num_params=2, units=["Ohm^-1 sec^a", ""]) def CPE(p, f): - """ defines a constant phase element + """defines a constant phase element Notes ----- @@ -181,15 +203,15 @@ def CPE(p, f): where :math:`Q` = p[0] and :math:`\\alpha` = p[1]. """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) Q, alpha = p[0], p[1] - Z = 1.0/(Q*(1j*omega)**alpha) + Z = 1.0 / (Q * (1j * omega) ** alpha) return Z -@element_metadata(num_params=2, units=['H sec', '']) +@element(num_params=2, units=["H sec", ""]) def La(p, f): - """ defines a modified inductance element as represented in [1] + """defines a modified inductance element as represented in [1] Notes ----- @@ -202,15 +224,15 @@ def La(p, f): [1] `EC-Lab Application Note 42, BioLogic Instruments (2019) `_. """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) L, alpha = p[0], p[1] - Z = (L*1j*omega)**alpha + Z = (L * 1j * omega) ** alpha return Z -@element_metadata(num_params=2, units=['Ohm', 'sec']) +@element(num_params=2, units=["Ohm", "sec"]) def G(p, f): - """ defines a Gerischer Element as represented in [1] + """defines a Gerischer Element as represented in [1] Notes --------- @@ -240,16 +262,16 @@ def G(p, f): G. Pudmich, and F. Tietz, Fuel Cells, 1, 256-264 (2001) `doi:10.1016/0013-4686(93)85083-B `_. - """ - omega = 2*np.pi*np.array(f) + """ + omega = 2 * np.pi * np.array(f) R_G, t_G = p[0], p[1] - Z = R_G/np.sqrt(1 + 1j*omega*t_G) + Z = R_G / np.sqrt(1 + 1j * omega * t_G) return Z -@element_metadata(num_params=3, units=['Ohm', 'sec', '']) +@element(num_params=3, units=["Ohm", "sec", ""]) def Gs(p, f): - """ defines a finite-length Gerischer Element as represented in [1] + """defines a finite-length Gerischer Element as represented in [1] Notes --------- @@ -264,17 +286,19 @@ def Gs(p, f): Solid State Ionics, 179, 647-660 (2008) `doi:10.1016/j.ssi.2008.04.024 `_. - """ - omega = 2*np.pi*np.array(f) + """ + omega = 2 * np.pi * np.array(f) R_G, t_G, phi = p[0], p[1], p[2] - Z = R_G/(np.sqrt(1 + 1j*omega*t_G) * - np.tanh(phi * np.sqrt(1 + 1j*omega*t_G))) + Z = R_G / ( + np.sqrt(1 + 1j * omega * t_G) + * np.tanh(phi * np.sqrt(1 + 1j * omega * t_G)) + ) return Z -@element_metadata(num_params=2, units=['Ohm', 'sec']) +@element(num_params=2, units=["Ohm", "sec"]) def K(p, f): - """ An RC element for use in lin-KK model + """An RC element for use in lin-KK model Notes ----- @@ -283,15 +307,15 @@ def K(p, f): Z = \\frac{R}{1 + j \\omega \\tau_k} """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) R, tau_k = p[0], p[1] - Z = R/(1 + 1j*omega*tau_k) + Z = R / (1 + 1j * omega * tau_k) return Z -@element_metadata(num_params=3, units=['Ohm', 'F sec^(gamma - 1)', '']) +@element(num_params=3, units=["Ohm", "F sec^(gamma - 1)", ""]) def TLMQ(p, f): - """ Simplified transmission-line model as defined in Eq. 11 of [1] + """Simplified transmission-line model as defined in Eq. 11 of [1] Notes ----- @@ -305,16 +329,16 @@ def TLMQ(p, f): `doi: 10.1016/10.1149/2.1141607jes `_. """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) Rion, Qs, gamma = p[0], p[1], p[2] - Zs = Qs*(1j*omega)**gamma - Z = np.sqrt(Rion/Zs)/np.tanh(np.sqrt(Rion*Zs)) + Zs = Qs * (1j * omega) ** gamma + Z = np.sqrt(Rion / Zs) / np.tanh(np.sqrt(Rion * Zs)) return Z -@element_metadata(num_params=4, units=['Ohm-m^2', 'Ohm-m^2', '', 'sec']) +@element(num_params=4, units=["Ohm-m^2", "Ohm-m^2", "", "sec"]) def T(p, f): - """ A macrohomogeneous porous electrode model from Paasch et al. [1] + """A macrohomogeneous porous electrode model from Paasch et al. [1] Notes ----- @@ -342,9 +366,9 @@ def T(p, f): `_. """ - omega = 2*np.pi*np.array(f) + omega = 2 * np.pi * np.array(f) A, B, a, b = p[0], p[1], p[2], p[3] - beta = (a + 1j*omega*b)**(1/2) + beta = (a + 1j * omega * b) ** (1 / 2) sinh = [] for x in beta: @@ -353,28 +377,27 @@ def T(p, f): else: sinh.append(1e10) - Z = A/(beta*np.tanh(beta)) + B/(beta*np.array(sinh)) + Z = A / (beta * np.tanh(beta)) + B / (beta * np.array(sinh)) return Z -circuit_elements = {key: eval(key) for key in set(globals())-set(initial_state) - if key not in non_element_functions} - - def get_element_from_name(name): - excluded_chars = '0123456789_' - return ''.join(char for char in name if char not in excluded_chars) + excluded_chars = "0123456789_" + return "".join(char for char in name if char not in excluded_chars) def typeChecker(p, f, name, length): assert isinstance(p, list), \ - 'in {}, input must be of type list'.format(name) + "in {}, input must be of type list".format(name) for i in p: - assert isinstance(i, (float, int, np.int32, np.float64)), \ - 'in {}, value {} in {} is not a number'.format(name, i, p) + assert isinstance( + i, (float, int, np.int32, np.float64) + ), "in {}, value {} in {} is not a number".format(name, i, p) for i in f: - assert isinstance(i, (float, int, np.int32, np.float64)), \ - 'in {}, value {} in {} is not a number'.format(name, i, f) - assert len(p) == length, \ - 'in {}, input list must be length {}'.format(name, length) + assert isinstance( + i, (float, int, np.int32, np.float64) + ), "in {}, value {} in {} is not a number".format(name, i, f) + assert len(p) == length, "in {}, input list must be length {}".format( + name, length + ) return diff --git a/impedance/tests/test_circuit_elements.py b/impedance/tests/test_circuit_elements.py index 1abb9934..c481f5b5 100644 --- a/impedance/tests/test_circuit_elements.py +++ b/impedance/tests/test_circuit_elements.py @@ -1,82 +1,110 @@ import string + import numpy as np import pytest -from impedance.models.circuits.elements import circuit_elements, s, p + +from impedance.models.circuits.elements import (OverwriteError, + circuit_elements, element, p, + s, ElementError) def test_each_element(): freqs = [0.001, 1.0, 1000] - correct_vals = {'R': [0.1, 0.1, 0.1], - 'C': [-1591.5494309189532j, - -1.5915494309189535j, - -0.0015915494309189533j], - 'L': [0.000628319j, 0.628319j, 628.319j], - 'W': [(1.26156626-1.26156626j), - (0.03989423-0.03989423j), - (0.00126157-0.00126157j)], - 'Wo': [(0.033333332999112786-79.57747433847442j), - (0.03300437046673635-0.08232866785870396j), - (0.0019947114020071634-0.0019947114020071634j)], - 'Ws': [(0.09999998-4.18878913e-05j), - (0.08327519-3.33838167e-02j), - (0.00199471-1.99471140e-03j)], - 'CPE': [(26.216236841407248-8.51817171087997j), - (6.585220960717244-2.139667994182814j), - (1.6541327179718126-0.537460300252313j)], - 'La': [(0.21769191+0.07073239j), - (0.86664712+0.28159072j), - (3.45018434+1.12103285j)], - 'G': [(0.09999994078244179-0.00006283179105931961j), - (0.07107755021941357-0.03427465211788068j), - (0.00199550459845528-0.0019939172581851707j)], - 'Gs': [(0.3432733166533134-0.00041895248193532704j), - (0.1391819314527732-0.16248466787637972j), - (0.0019955029598887875-0.0019939170758457437j)], - 'TLMQ': [(20.42237173-10.38874276j), - (2.6000937-1.30789949j), - (0.35594139-0.16491599j)], - 'T': [(1.00041-0.00837309j), - (0.0156037-0.114062j), - (0.00141056-0.00141039j)], - 'K': [(0.099999842086579 - 0.000125663507704j), - (0.038772663673915 - 0.048723166143232j), - (6.332569967499333e-08 - 7.957742115295703e-05j)]} + correct_vals = { + "R": [0.1, 0.1, 0.1], + "C": [ + -1591.5494309189532j, + -1.5915494309189535j, + -0.0015915494309189533j, + ], + "L": [0.000628319j, 0.628319j, 628.319j], + "W": [ + (1.26156626 - 1.26156626j), + (0.03989423 - 0.03989423j), + (0.00126157 - 0.00126157j), + ], + "Wo": [ + (0.033333332999112786 - 79.57747433847442j), + (0.03300437046673635 - 0.08232866785870396j), + (0.0019947114020071634 - 0.0019947114020071634j), + ], + "Ws": [ + (0.09999998 - 4.18878913e-05j), + (0.08327519 - 3.33838167e-02j), + (0.00199471 - 1.99471140e-03j), + ], + "CPE": [ + (26.216236841407248 - 8.51817171087997j), + (6.585220960717244 - 2.139667994182814j), + (1.6541327179718126 - 0.537460300252313j), + ], + "La": [ + (0.21769191 + 0.07073239j), + (0.86664712 + 0.28159072j), + (3.45018434 + 1.12103285j), + ], + "G": [ + (0.09999994078244179 - 0.00006283179105931961j), + (0.07107755021941357 - 0.03427465211788068j), + (0.00199550459845528 - 0.0019939172581851707j), + ], + "Gs": [ + (0.3432733166533134 - 0.00041895248193532704j), + (0.1391819314527732 - 0.16248466787637972j), + (0.0019955029598887875 - 0.0019939170758457437j), + ], + "TLMQ": [ + (20.42237173 - 10.38874276j), + (2.6000937 - 1.30789949j), + (0.35594139 - 0.16491599j), + ], + "T": [ + (1.00041 - 0.00837309j), + (0.0156037 - 0.114062j), + (0.00141056 - 0.00141039j), + ], + "K": [ + (0.099999842086579 - 0.000125663507704j), + (0.038772663673915 - 0.048723166143232j), + (6.332569967499333e-08 - 7.957742115295703e-05j), + ], + } input_vals = [0.1, 0.2, 0.3, 0.4] for key, f in circuit_elements.items(): # don't test the outputs of series and parallel functions - if key not in ['s', 'p']: + if key not in ["s", "p"]: num_inputs = f.num_params val = f(input_vals[:num_inputs], freqs) assert np.isclose(val, correct_vals[key]).all() # check for typing: with pytest.raises(AssertionError): - f = circuit_elements['R'] + f = circuit_elements["R"] f(1, 2) # test for handling more wrong inputs with pytest.raises(AssertionError): - f(['hi'], ['yes', 'hello']) + f(["hi"], ["yes", "hello"]) # Test no overflow in T at high frequencies with pytest.warns(None) as record: - circuit_elements['T']([1, 2, 50, 100], [10000]) + circuit_elements["T"]([1, 2, 50, 100], [10000]) assert not record def test_s(): - a = np.array([5 + 6*1j, 2 + 3*1j]) - b = np.array([5 + 6*1j, 2 + 3*1j]) + a = np.array([5 + 6 * 1j, 2 + 3 * 1j]) + b = np.array([5 + 6 * 1j, 2 + 3 * 1j]) - answer = np.array([10 + 12*1j, 4 + 6*1j]) + answer = np.array([10 + 12 * 1j, 4 + 6 * 1j]) assert np.isclose(s([a, b]), answer).all() def test_p(): - a = np.array([5 + 6*1j, 2 + 3*1j]) - b = np.array([5 + 6*1j, 2 + 3*1j]) + a = np.array([5 + 6 * 1j, 2 + 3 * 1j]) + b = np.array([5 + 6 * 1j, 2 + 3 * 1j]) - answer = np.array([2.5 + 3*1j, 1 + 1.5*1j]) + answer = np.array([2.5 + 3 * 1j, 1 + 1.5 * 1j]) assert np.isclose(p([a, b]), answer).all() @@ -87,5 +115,97 @@ def test_element_function_names(): for elem in circuit_elements.keys(): for char in elem: - assert char in letters, \ - f'{char} in {elem} is not in the allowed set of {letters}' + assert ( + char in letters + ), f"{char} in {elem} is not in the allowed set of {letters}" + + +def test_changing_base_functions_fails(): + with pytest.raises(ElementError): + @element(num_params=1, units=["Ohm"]) + def s(p, f): + # try redefining the series + return np.nan + + +def test_add_element(): + # checks if you can add your own custom element + assert "NE" not in circuit_elements + + @element(num_params=1, units=["Ohm"]) + def NE(p, f): + """definitely a new circuit element no one has seen before + + Notes + --------- + .. math:: + + Z = R + + """ + R = p[0] + Z = np.array(len(f) * [R]) + return Z + + assert "NE" in circuit_elements + + +def test_add_element_overwrite_fails(): + # checks if you can add your own custom element + # and then overwriting it raises an OverwriteError + assert "NE2" not in circuit_elements + + @element(num_params=1, units=["Ohm"]) + def NE2(p, f): + """definitely a new circuit element no one has seen before + + Notes + --------- + .. math:: + + Z = R + + """ + R = p[0] + Z = np.array(len(f) * [R]) + return Z + + assert "NE2" in circuit_elements + with pytest.raises(OverwriteError): + # try to create the same element again without overwrite + @element(num_params=1, units=["Ohm"]) # noqa: F811 + def NE2(p, f): + """definitely a new circuit element no one has seen before + + Notes + --------- + .. math:: + + Z = R + + """ + R = p[0] + Z = np.array(len(f) * [R]) + return Z + + +def test_add_element_overwrite(): + # checks if you can add your own custom element + # and then overwriting it is allowed with correct kwarg + assert "NE3" not in circuit_elements + + @element(num_params=1, units=["Ohm"]) + def NE3(p, f): + return [p * ff for ff in f] + + assert "NE3" in circuit_elements + assert circuit_elements["NE3"]([1], [1]) == [[1]] + # try to create the same element again with overwrite + + @element(num_params=1, units=["Ohm"], overwrite=True) # noqa: F811 + def NE3(p, f): + # feel free to change to a better test + return [p * ff * 2 for ff in f] + + assert "NE3" in circuit_elements + assert circuit_elements["NE3"]([1], [1]) == [[1, 1]] diff --git a/pylama.ini b/pylama.ini new file mode 100644 index 00000000..7933e27d --- /dev/null +++ b/pylama.ini @@ -0,0 +1,6 @@ +[pylama:pycodestyle] +max_line_length = 80 + +[pylama:pylint] +max_line_length = 80 +disable = R \ No newline at end of file From e666b1298c527450570c5a89934ed73605c76efb Mon Sep 17 00:00:00 2001 From: Matt Murbach Date: Thu, 2 Feb 2023 20:23:42 -0800 Subject: [PATCH 17/23] replace spaces in circuit string for custom circuits (#247) --- impedance/models/circuits/circuits.py | 2 +- impedance/tests/test_circuits.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/impedance/models/circuits/circuits.py b/impedance/models/circuits/circuits.py index 70d402bb..b670d198 100644 --- a/impedance/models/circuits/circuits.py +++ b/impedance/models/circuits/circuits.py @@ -431,7 +431,7 @@ def __init__(self, circuit='', **kwargs): """ super().__init__(**kwargs) - self.circuit = circuit + self.circuit = circuit.replace(" ", "") circuit_len = calculateCircuitLength(self.circuit) diff --git a/impedance/tests/test_circuits.py b/impedance/tests/test_circuits.py index 088e5776..2c10d8ba 100644 --- a/impedance/tests/test_circuits.py +++ b/impedance/tests/test_circuits.py @@ -185,3 +185,8 @@ def test_CustomCircuit(): # incorrect circuit element in circuit with pytest.raises(ValueError): custom_circuit = CustomCircuit('R0-NotAnElement', initial_guess=[1, 2]) + + # space in circuit string + circuit = circuit = 'R0-p(R1, C1)' + initial_guess = [1, 2, 3] + circuit = CustomCircuit(circuit, initial_guess=initial_guess) From aaa9617d2b99400761335f7c52d3b2d5e8df3b3b Mon Sep 17 00:00:00 2001 From: Brian Gerwe Date: Fri, 10 Feb 2023 08:12:53 -0800 Subject: [PATCH 18/23] Adds flake8 to dependencies. 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2001 From: Brian Gerwe Date: Mon, 13 Feb 2023 21:18:13 -0800 Subject: [PATCH 19/23] Update pyproject to format for poetry >1.2. Add flake8 to dev requirements --- poetry.lock | 2 +- pyproject.toml | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index aaed8825..9d556c88 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1850,4 +1850,4 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools" [metadata] lock-version = "2.0" python-versions = ">=3.7,<3.11" -content-hash = "5650a626801645b62c25749814fe984d762115864ddce5b135ac474786c18791" +content-hash = "af06e656b4bdb21d0d13ea3aae659c2316e44f5123c0b7106f18621b1e9b5742" diff --git a/pyproject.toml b/pyproject.toml index 1a598631..dd7ae239 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,15 +12,13 @@ scipy = ">=1.0" matplotlib = ">=3.0" altair = "^4.2.0" -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] coveralls = "3.2.0" numpydoc = "^1.5.0" nbsphinx = "^0.8.9" pytest = ">=4.6" pytest-cov = "^4.0.0" - -[tool.poetry.group.dev.dependencies] -flake8 = ">5.0,<6.0" +flake8 = "<6.0.0" [build-system] requires = ["poetry-core>=1.0.0"] From 0a767447a1da15ffdacf5d8b5674234a8ad69942 Mon Sep 17 00:00:00 2001 From: Brian Gerwe Date: Mon, 13 Feb 2023 21:21:15 -0800 Subject: [PATCH 20/23] Change poetry version in build action --- .github/actions/build_impedance/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/build_impedance/action.yml b/.github/actions/build_impedance/action.yml index b8012cb5..e7dc1cfa 100644 --- a/.github/actions/build_impedance/action.yml +++ b/.github/actions/build_impedance/action.yml @@ -14,7 +14,7 @@ runs: - name: Install Poetry run: | - curl -sSL https://install.python-poetry.org | python3 - --version 1.1.14 + curl -sSL https://install.python-poetry.org | python3 - --version 1.3.2 echo "$HOME/.poetry/bin" >> $GITHUB_PATH # add poetry to PATH. shell: bash From bd501fde3e8a90205bda27803dfbec7ccd23f066 Mon Sep 17 00:00:00 2001 From: Brian Gerwe Date: Mon, 13 Feb 2023 21:31:28 -0800 Subject: [PATCH 21/23] include python 3.11 in project specs --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dd7ae239..c241ef71 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = ["impedance.py developers "] license = "MIT license" [tool.poetry.dependencies] -python = ">=3.7,<3.11" +python = ">=3.7,<3.12" numpy = ">=1.14" scipy = ">=1.0" matplotlib = ">=3.0" From 42fcc7be298e67a210cdda87cd51f387a874edf2 Mon Sep 17 00:00:00 2001 From: Brian Gerwe Date: Mon, 13 Feb 2023 22:06:14 -0800 Subject: [PATCH 22/23] resync lock file --- poetry.lock | 125 +++++++++++++++++++++++----------------------------- 1 file changed, 56 insertions(+), 69 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9d556c88..264ed94c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -929,43 +929,40 @@ files = [ [[package]] name = "numpy" -version = "1.21.6" +version = "1.21.1" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false -python-versions = ">=3.7,<3.11" -files = [ - 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