Prep LFPy-2.3 release (#439)

* bump version * test against lfpykit>=0.5 * updated notebooks * add linter for Dockerfile * updated Dockerfile * hadolint * hadolint
LFPy · Dec 15, 2022 · bde519b · bde519b
1 parent e441281
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diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
@@ -0,0 +1,16 @@
+name: Dockerfile Linter
+
+on: [push, pull_request]
+
+jobs:
+  hadolint:
+    name: runner / hadolint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v1
+      - name: hadolint
+        uses: reviewdog/action-hadolint@v1
+        with:
+          reporter: github-pr-review # Default is github-pr-check
+          fail_on_error: true
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ conda:
   environment: doc/environment.yml
 
 python:
-    version: 3
+    version: "3"
     install:
         - method: pip
           path: .
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ authors:
     given-names: "Torbjørn V."
     orcid: "https://orcid.org/0000-0001-9080-8502"
 title: "LFPy"
-version: 2.2.5
-doi: "10.5281/zenodo.6346541"
-date-released: 2021-11-17
+version: 2.2.6
+doi: "10.5281/zenodo.6414521"
+date-released: 2022-04-05
 url: "https://github.com/LFPy/LFPy"
diff --git a/Dockerfile b/Dockerfile
@@ -1,52 +1,29 @@
 # -------- base ---------
-FROM buildpack-deps:hirsute AS base
+FROM buildpack-deps:jammy AS base
 
 RUN apt-get update && \
     apt-get install --no-install-recommends -y \
-    python3-dev=3.9.4-1 \
-    python3-scipy=1.6.0-2 \
-    python3-matplotlib=3.3.4-1 \
-    python3-pytest=6.0.2-2ubuntu1 \
-    python3-pip=20.3.4-1ubuntu2 \
-    python3-pandas=1.1.5+dfsg-2 \
-    cython3=0.29.21-1ubuntu3 \
-    jupyter=4.7.1-1\
-    jupyter-notebook=6.2.0-1 \
-    ipython3=7.20.0-1 \
-    cmake=3.18.4-2ubuntu1 \
-    bison=2:3.7.5+dfsg-1 \
-    flex=2.6.4-8 \
-    libmpich-dev=3.4.1-3build1 \
-    libncurses-dev=6.2+20201114-2build1 \
+    python3-dev=3.10.6-1~22.04 \
+    python3-scipy=1.8.0-1exp2ubuntu1 \
+    python3-matplotlib=3.5.1-2build1 \
+    python3-pytest=6.2.5-1ubuntu2 \
+    python3-pip=22.0.2+dfsg-1 \
+    python3-pandas=1.3.5+dfsg-3 \
+    python3-h5py=3.6.0-2build1 \
+    cython3=0.29.28-1ubuntu3 \
+    cmake=3.22.1-1ubuntu1.22.04.1 \
+    bison=2:3.8.2+dfsg-1build1 \
+    flex=2.6.4-8build2 \
+    libmpich-dev=4.0-3 \
+    libncurses-dev=6.3-2 \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
-    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 && \
-    update-alternatives --install /usr/bin/ipython ipython /usr/bin/ipython3 10
-
-# --- install NEURON from source
-# (only way to get builds on arm64/aarch64 hosts working) -------
-RUN git clone --depth 1 -b 8.0.0 https://github.com/neuronsimulator/nrn.git /usr/src/nrn
-RUN mkdir nrn-bld
-
-RUN cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/ \
-  -DCURSES_NEED_NCURSES=ON \
-  -DNRN_ENABLE_INTERVIEWS=OFF \
-  -DNRN_ENABLE_MPI=ON \
-  -DNRN_ENABLE_RX3D=ON \
-  -DNRN_ENABLE_PYTHON=ON \
-  -S /usr/src/nrn \
-  -B nrn-bld
-
-RUN cmake --build nrn-bld --parallel 4 --target install
-
-# add nrnpython to PYTHONPATH
-ENV PYTHONPATH /usr/local/lib/python:${PYTHONPATH}
-
-# clean up
-RUN rm -r /usr/src/nrn
-RUN rm -r nrn-bld
+    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 
 # --- Install LFPy ----
-RUN pip install git+https://github.com/LFPy/LFPy@master#egg=LFPy
+RUN pip install --no-cache-dir mpi4py==3.1.4 && \
+  pip install --no-cache-dir jupyterlab==3.5.1 && \
+  pip install --no-cache-dir git+https://github.com/LFPy/LFPy@master#egg=LFPy && \
+  pip cache purge
diff --git a/LFPy/version.py b/LFPy/version.py
@@ -1 +1 @@
-version = "2.3.dev"
+version = "2.3rc0"
diff --git a/examples/LFPy-example-01.ipynb b/examples/LFPy-example-01.ipynb
diff --git a/examples/LFPy-example-02.ipynb b/examples/LFPy-example-02.ipynb
diff --git a/examples/LFPy-example-03.ipynb b/examples/LFPy-example-03.ipynb
diff --git a/examples/LFPy-example-04.ipynb b/examples/LFPy-example-04.ipynb
diff --git a/examples/LFPy-example-05.ipynb b/examples/LFPy-example-05.ipynb
diff --git a/examples/LFPy-example-06.ipynb b/examples/LFPy-example-06.ipynb
diff --git a/examples/LFPy-example-07.ipynb b/examples/LFPy-example-07.ipynb
diff --git a/examples/LFPy-example-08.ipynb b/examples/LFPy-example-08.ipynb
diff --git a/examples/LFPy-example-09.ipynb b/examples/LFPy-example-09.ipynb
diff --git a/examples/LFPy-example-10.ipynb b/examples/LFPy-example-10.ipynb
diff --git a/examples/LFPy-example-11.ipynb b/examples/LFPy-example-11.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -6,5 +6,4 @@ Cython>=0.20
 h5py>=2.5
 matplotlib>=2.0
 neuron>=7.7.2
-# LFPykit>=0.5.dev
-git+https://github.com/LFPy/LFPykit@master#egg=lfpykit
+LFPykit>=0.5
diff --git a/setup.py b/setup.py
@@ -86,7 +86,7 @@
         'scipy>=0.14',
         'Cython>=0.20',
         'h5py>=2.5',
-        'lfpykit@git+https://github.com/LFPy/LFPykit.git#egg=lfpykit'
+        'lfpykit>=0.5'
     ],
     extras_require={'tests': ['pytest'],
                     'docs': ['sphinx', 'numpydoc', 'sphinx_rtd_theme']