Merge branch 'master' into feature/newFilter

# Conflicts:
#	neo/core/container.py
#	neo/test/coretest/test_container.py

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us fix problems
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour, preferably providing a simple code example (if the error happens in the middle of some complex code, please try to find a simpler, minimal example that demonstrates the error), and showing the full traceback.
+
+If the error occurs when reading a file that you can't share publicly, please let us know, and we'll get in touch to discuss sharing it privately.
+
+**Expected behaviour**
+If the bug is incorrect behaviour, rather than an unexpected Exception, please give a clear and concise description of what you expected to happen.
+
+**Environment:**
+ - OS: [e.g. macOS, Linux, Windows]
+ - Python version
+ - Neo version
+ - NumPy version
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/confusing-documentation.md

@@ -0,0 +1,17 @@
+---
+name: Confusing documentation
+about: Let us know if the documentation is confusing or incorrect
+title: ''
+labels: Documentation
+assignees: ''
+
+---
+
+**Which page is the problem on?**
+The URL of the documentation page where the problem is, and either copy-paste the confusing text (for a short section of text), or give the first few and last few words (for a long section).
+
+**What is the problem?**
+Is the documentation (a) confusing or (b) incorrect? In what way?
+
+**Suggestions for fixing the problem**
+If the documentation is confusing, can you suggest an improvement? If the documentation is incorrect, what should it say instead?

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea to improve Neo
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/caches_cron_job.yml

@@ -0,0 +1,109 @@
+name: Create caches for ephy_testing_data and conda env
+
+on:
+  workflow_dispatch: # Workflow can be triggered manually via GH actions webinterface
+  push:  # When something is pushed into master this checks if caches need to re-created
+    branches:
+      - master
+  schedule:
+    - cron: "0 12 * * *"  # Daily at noon UTC
+
+jobs:
+
+  create-conda-env-cache-if-missing:
+    name: Caching conda env
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: true
+    defaults:
+      # by default run in bash mode (required for conda usage)
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Get current year-month
+        id: date
+        run: |
+          echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
+
+      - name: Get current dependencies hash
+        id: dependencies
+        run: |
+          echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
+
+      - uses: actions/cache@v3
+        # the cache for python package is reset:
+        #   * every month
+        #   * when package dependencies change
+        id: cache-conda-env
+        with:
+          path: /usr/share/miniconda/envs/neo-test-env
+          key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
+
+      - name: Cache found?
+        run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
+
+      # activate environment if not restored from cache
+      - uses: conda-incubator/setup-miniconda@v2.2.0
+        if: steps.cache-conda-env.outputs.cache-hit != 'true'
+        with:
+          activate-environment: neo-test-env
+          environment-file: environment_testing.yml
+          python-version: 3.9
+
+      - name: Create the conda environment to be cached
+        if: steps.cache-conda-env.outputs.cache-hit != 'true'
+        # create conda env, configure git and install pip, neo and test dependencies from master
+        # for PRs that change dependencies, this environment will be updated in the test workflow
+        run: |
+          git config --global user.email "neo_ci@fake_mail.com"
+          git config --global user.name "neo CI"
+          python -m pip install -U pip  # Official recommended way
+          pip install --upgrade -e .[test]
+
+  create-data-cache-if-missing:
+    name: Caching data env
+    runs-on: "ubuntu-latest"
+    steps:
+
+      - name: Get current hash (SHA) of the ephy_testing_data repo
+        id: ephy_testing_data
+        run: |
+          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
+
+      - uses: actions/cache@v3
+        # Loading cache of ephys_testing_dataset
+        id: cache-datasets
+        with:
+          path: ~/ephy_testing_data
+          key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
+
+      - name: Cache found?
+        run: echo "Cache-hit == ${{steps.cache-datasets.outputs.cache-hit == 'true'}}"
+
+      - name: Installing datalad and git-annex
+        if: steps.cache-datasets.outputs.cache-hit != 'true'
+        run: |
+          git config --global user.email "neo_ci@fake_mail.com"
+          git config --global user.name "neo CI"
+          python -m pip install -U pip  # Official recommended way
+          pip install datalad-installer
+          datalad-installer --sudo ok git-annex --method datalad/packages
+          pip install datalad
+          git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
+
+      - name: Download dataset
+        if: steps.cache-datasets.outputs.cache-hit != 'true'
+        # Download repository and also fetch data
+        run: |
+          cd ~
+          datalad install --recursive --get-data https://gin.g-node.org/NeuralEnsemble/ephy_testing_data
+
+      - name: Show size of the cache to assert data is downloaded
+        run: |
+          cd ~
+          pwd
+          du -hs ephy_testing_data
+          cd ephy_testing_data
+          pwd

.github/workflows/core-test.yml

@@ -4,12 +4,17 @@ on:
   pull_request:
     branches: [master]
     types: [synchronize, opened, reopened, ready_for_review]
+    paths:
+      - 'neo/core/**'
+      - 'pyproject.toml'
 
   # run checks on any change of master, including merge of PRs
   push:
     branches: [master]
 
-
+concurrency: # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   multi-os-python-numpy:
@@ -19,21 +24,28 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        # "macos-latest", 
-        python-version: ['3.7', '3.8', '3.9']
-        numpy-version: ['1.16.6', '1.17.5', '1.18.5', '1.19.5', '1.20.3', '1.21.5', '1.22.3']
+        # "macos-latest",
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        numpy-version: ['1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1']
         exclude:
-           - python-version: '3.7'
-             numpy-version: '1.22.3'
-
+           - python-version: '3.10'
+             numpy-version: '1.19.5'
+           - python-version: '3.10'
+             numpy-version: '1.20.3'
+           - python-version: '3.11'
+             numpy-version: '1.19.5'
+           - python-version: '3.11'
+             numpy-version: '1.20.3'
+           - python-version: '3.11'
+             numpy-version: '1.21.6'
     steps:
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v2
+          uses: actions/setup-python@v4
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Checkout repository
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
 
         - name: Install numpy ${{ matrix.numpy-version }}
           run: |

.github/workflows/ebrains.yml

@@ -0,0 +1,30 @@
+name: Mirror to EBRAINS
+
+# Configure the events that are going to trigger tha automated update of the mirror
+on:
+  push:
+    branches: [ master ]
+
+# Configure what will be updated
+jobs:
+  # set the job name
+  to_ebrains:
+    runs-on: ubuntu-latest
+    steps:
+      # this task will push the master branch of the source_repo (github) to the
+      # destination_repo (ebrains gitlab)
+      - name: syncmaster
+        uses: wei/git-sync@v3
+        with:
+          source_repo: https://github.com/NeuralEnsemble/python-neo
+          source_branch: "master"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
+          destination_branch: "main"
+      # this task will push all tags from the source_repo to the destination_repo
+      - name: synctags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: https://github.com/NeuralEnsemble/python-neo
+          source_branch: "refs/tags/*"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
+          destination_branch: "refs/tags/*"

.github/workflows/io-test.yml

@@ -1,80 +1,106 @@
 name: NeoIoTest
 
 on:
-  pull_request:
-    branches: [master]
-    types: [synchronize, opened, reopened, ready_for_review]
-
-  # run checks on any change of master, including merge of PRs
-  push:
-    branches: [master]
+  workflow_call:
+    inputs:
+      os:
+        required: true
+        type: string
 
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build-and-test:
-    name: Test on (${{ matrix.os }})
-    runs-on: ${{ matrix.os }}
+    name: Test on (${{ inputs.os }})
+    runs-on: ${{ inputs.os }}
     strategy:
       fail-fast: true
       matrix:
-        # "macos-latest", "windows-latest"
-        os: ["ubuntu-latest", ]
-        python-version: ['3.8', ]
+        python-version: ['3.9', ]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
         shell: bash -l {0}
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - name: Get ephy_testing_data current head hash
         # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
-        id: vars
+        id: ephy_testing_data
         run: |
-          echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache@v3
+      - uses: actions/cache/restore@v3
         # Loading cache of ephys_testing_dataset
         id: cache-datasets
         with:
           path: ~/ephy_testing_data
-          key: ${{ runner.os }}-datasets-${{ steps.vars.outputs.HASH_EPHY_DATASET }}
+          key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
+          restore-keys: ${{ runner.os }}-datasets-
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v2.2.0
         with:
           activate-environment: neo-test-env
           python-version: ${{ matrix.python-version }}
-          clean-patched-environment-file: false
 
-      - uses: actions/cache@v3
+      - name: Get current dependencies hash
+        id: dependencies
+        run: |
+          echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
+
+      - uses: actions/cache/restore@v3
         # the cache for python package is reset:
         #   * every month
-        #   * when requirements/requirements_testing change
+        #   * when package dependencies change
         id: cache-conda-env
         with:
           path: /usr/share/miniconda/envs/neo-test-env
-          key: ${{ runner.os }}-conda-env-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ hashFiles('**/environment_testing.txt') }}-${{ steps.date.outputs.date }}
+          key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
+          # restore-keys match any key that starts with the restore-key
+          restore-keys: |
+            ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
+            ${{ runner.os }}-conda-env-
 
       - name: Install testing dependencies
-        # testing environment is only installed if no cache was found
+        # testing environment is only created from yml if no cache was found
+        # restore-key hits should result in `cache-hit` == 'false'
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          conda env update neo-test-env --file environment_testing.yml
+          conda env update --name neo-test-env --file environment_testing.yml --prune
 
       - name: Configure git
         run: |
           git config --global user.email "neo_ci@fake_mail.com"
           git config --global user.name "neo CI"
 
-      - name: Install neo
+      - name: Install neo including dependencies
+        # installation with dependencies is only required if no cache was found
+        # restore-key hits should result in `cache-hit` == 'false'
+        if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
           pip install --upgrade -e .
+          pip install .[test]
+
+      - name: Install neo without dependencies
+        # only installing neo version to test as dependencies should be in cached conda env already
+        if: steps.cache-conda-env.outputs.cache-hit == 'true'
+        run: |
+          pip install --no-dependencies -e .
+
+      - name: Install wine
+        run: |
+          sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+          sudo dpkg --add-architecture i386
+          sudo apt-get update -qq
+          sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
 
       - name: Test with pytest
         run: |