From b326783acfd8c7642fceea4b5b4df8c3d7ff532f Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Mon, 19 Sep 2022 17:55:49 +0200 Subject: [PATCH 1/9] updated versions in github actions --- .github/workflows/ci.yaml | 4 ++-- .github/workflows/package.yaml | 4 ++-- .github/workflows/website.yaml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index b759059..975d51f 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -15,10 +15,10 @@ jobs: runs-on: ${{ matrix.os }} steps: - name: 🛒 Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: 🐍 Get Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 - name: 🚚 Get Dependencies run: | diff --git a/.github/workflows/package.yaml b/.github/workflows/package.yaml index 2218f4c..67c8820 100644 --- a/.github/workflows/package.yaml +++ b/.github/workflows/package.yaml @@ -9,10 +9,10 @@ jobs: runs-on: ubuntu-latest steps: - name: 🛒 Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: 🐍 Get Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 - name: 🛠️ Setup Build run: python -m pip install build --user diff --git a/.github/workflows/website.yaml b/.github/workflows/website.yaml index 77484aa..cdd0b37 100644 --- a/.github/workflows/website.yaml +++ b/.github/workflows/website.yaml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: 🛒 Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: ✨ Setup Hugo env: From db7a08940137a39b44faedbb41a55a703f599f3f Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Tue, 20 Sep 2022 09:28:59 +0200 Subject: [PATCH 2/9] using specific function to transpose matrix --- src/pyabf/abf.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/pyabf/abf.py b/src/pyabf/abf.py index a0ea509..63aaefd 100644 --- a/src/pyabf/abf.py +++ b/src/pyabf/abf.py @@ -472,8 +472,7 @@ def _loadAndScaleData(self, fb: BufferedReader): nRows = self.channelCount nCols = int(self.dataPointCount/self.channelCount) raw = np.reshape(raw, (nCols, nRows)) - raw = np.rot90(raw) - raw = raw[::-1] + raw = np.transpose(raw) # if data is int, scale it to float32 so we can scale it self.data = raw.astype(np.float32) From 5e1a84d9dbeddf3e0db2d437344820cd2e93b795 Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Tue, 20 Sep 2022 14:45:05 +0200 Subject: [PATCH 3/9] use different versions of python --- .github/workflows/ci.yaml | 3 +++ .github/workflows/package.yaml | 2 ++ 2 files changed, 5 insertions(+) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 975d51f..dd195a1 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -11,6 +11,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] + python-version: ["3.7", "3.8", "3.9", "3.10", "3.x"] runs-on: ${{ matrix.os }} steps: @@ -19,6 +20,8 @@ jobs: - name: 🐍 Get Python uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} - name: 🚚 Get Dependencies run: | diff --git a/.github/workflows/package.yaml b/.github/workflows/package.yaml index 67c8820..79b6c3d 100644 --- a/.github/workflows/package.yaml +++ b/.github/workflows/package.yaml @@ -13,6 +13,8 @@ jobs: - name: 🐍 Get Python uses: actions/setup-python@v4 + with: + python-version: "3.x" - name: 🛠️ Setup Build run: python -m pip install build --user From f16b1efb13b0594b8028c785086534dca955a4d1 Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Tue, 20 Sep 2022 17:21:06 +0200 Subject: [PATCH 4/9] changed python version matrix --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index dd195a1..fa2a848 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -11,7 +11,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.7", "3.8", "3.9", "3.10", "3.x"] + python-version: ["3.6", "3.x"] runs-on: ${{ matrix.os }} steps: From 190808c04910e0ef5269a732fcf6bb6ad298092c Mon Sep 17 00:00:00 2001 From: lucarossi147 <53348738+lucarossi147@users.noreply.github.com> Date: Tue, 20 Sep 2022 17:24:56 +0200 Subject: [PATCH 5/9] Update ci.yaml --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index fa2a848..0d15719 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -11,7 +11,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.6", "3.x"] + python-version: ["3.6.x", "3.x"] runs-on: ${{ matrix.os }} steps: From f0966d3d2e6d3b518b436c5128158cfd3e5e219e Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Wed, 21 Sep 2022 15:40:37 +0200 Subject: [PATCH 6/9] macos sucks --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index fa2a848..614b10f 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -11,7 +11,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.6", "3.x"] + python-version: ["3.8", "3.x"] runs-on: ${{ matrix.os }} steps: From 1bf0d5be03760aa876a20045d52102683eec2eae Mon Sep 17 00:00:00 2001 From: Luca Rossi Date: Wed, 21 Sep 2022 15:47:01 +0200 Subject: [PATCH 7/9] fixed multi channel bug in sweep with different length --- src/pyabf/abf.py | 6 +++--- tests/test_sweepHashes.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/pyabf/abf.py b/src/pyabf/abf.py index 63aaefd..253889d 100644 --- a/src/pyabf/abf.py +++ b/src/pyabf/abf.py @@ -641,9 +641,9 @@ def setSweep(self, pointCount = self.sweepPointCount else: pointStart = 0 - for i in range(1, sweepNumber): - pointStart += self._synchArraySection.lLength[i-1] - pointCount = self._synchArraySection.lLength[sweepNumber] + for i in range(sweepNumber): + pointStart += self._synchArraySection.lLength[i]//self.channelCount + pointCount = self._synchArraySection.lLength[sweepNumber]//self.channelCount pointEnd = pointStart + pointCount # load the actual sweep data diff --git a/tests/test_sweepHashes.py b/tests/test_sweepHashes.py index 2a5b73e..38f3350 100644 --- a/tests/test_sweepHashes.py +++ b/tests/test_sweepHashes.py @@ -1275,11 +1275,11 @@ knownAbfSweepValues["2020_03_02_0000.abf SW15 CH1"] = "20000, 9.46044922, -0.30517578, 259.74499512" knownAbfSweepValues["2020_06_16_0000.abf SW0 CH0"] = "3540, 0.91552734, 0.00000000, 0.34947360" -knownAbfSweepValues["2020_06_16_0000.abf SW1 CH0"] = "70040, 0.91552734, 0.61035156, 0.34824026" -knownAbfSweepValues["2020_06_16_0000.abf SW2 CH0"] = "16040, -0.30517578, 0.61035156, 0.35196608" +knownAbfSweepValues["2020_06_16_0000.abf SW1 CH0"] = "70040, -0.30517578, 0.30517578, 0.34824499" +knownAbfSweepValues["2020_06_16_0000.abf SW2 CH0"] = "16040, 0.61035156, 0.30517578, 0.35050380" knownAbfSweepValues["2020_06_16_0001.abf SW0 CH0"] = "22040, 0.61035156, 0.00000000, 0.34784842" -knownAbfSweepValues["2020_06_16_0001.abf SW1 CH0"] = "11040, 0.61035156, 0.61035156, 0.34771526" +knownAbfSweepValues["2020_06_16_0001.abf SW1 CH0"] = "11040, -0.30517578, 0.91552734, 0.35148475" knownAbfSweepValues["abf1_with_tags.abf SW0 CH0"] = "18000000, -34.54589462, -80.74950409, 6.65401363" @@ -2659,4 +2659,4 @@ knownAbfSweepValues["test_0001.abf SW0 CH12"] = "12896, -0.00122070, -0.00122070, 0.00017642" knownAbfSweepValues["test_0001.abf SW0 CH13"] = "12896, 0.00152588, 0.00183105, 0.00016845" knownAbfSweepValues["test_0001.abf SW0 CH14"] = "12896, -0.21362305, -0.18310547, 0.01735568" -knownAbfSweepValues["test_0001.abf SW0 CH15"] = "12896, 0.00000000, 0.00000000, 0.00191588" \ No newline at end of file +knownAbfSweepValues["test_0001.abf SW0 CH15"] = "12896, 0.00000000, 0.00000000, 0.00191588" From 0c582e11220e8b59804b8d1fcff939c8afe91a24 Mon Sep 17 00:00:00 2001 From: Scott W Harden Date: Mon, 26 Sep 2022 20:18:34 -0400 Subject: [PATCH 8/9] CI: Test using python 3.7 3.6 is technically supported by pyabf but is not supported by the action runner --- .github/workflows/ci.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index a6632d6..bc9da40 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -7,11 +7,11 @@ on: jobs: test: - name: Test on ${{ matrix.os }} + name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.8", "3.x"] + python-version: ["3.7", "3.x"] runs-on: ${{ matrix.os }} steps: From be6121ccee9276c04a43654384f8524a9cb6ca86 Mon Sep 17 00:00:00 2001 From: Scott W Harden Date: Mon, 26 Sep 2022 20:20:03 -0400 Subject: [PATCH 9/9] pyabf 2.3.7 --- src/pyabf/__init__.py | 2 +- src/setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pyabf/__init__.py b/src/pyabf/__init__.py index dd6064b..7cb8e80 100644 --- a/src/pyabf/__init__.py +++ b/src/pyabf/__init__.py @@ -5,7 +5,7 @@ Documentation and code examples, and more can be found at: https://github.com/swharden/pyABF """ -__version__ = '2.3.6' +__version__ = '2.3.7' import sys import os diff --git a/src/setup.py b/src/setup.py index 881746a..c242de3 100644 --- a/src/setup.py +++ b/src/setup.py @@ -14,7 +14,7 @@ # standard pypi stuff setup( name='pyabf', - version='2.3.6', + version='2.3.7', author='Scott W Harden', author_email='SWHarden@gmail.com', python_requires='>=3.6',