8.11.0 (#517)

* update pip * add method for checking availability of internet connection * move update check to separate thread * version number / changelog * transfer_data CLI with argparse * Update CHANGELOG.md * prepare thread-worker for fetching subject details * fix transfer test using local lab: use mock function instead of settings * get rid of rsync-path * add md5 check to copy_folders * doc-strings & type-hints * reorganize handling of CLI transfer scripts * documentation * Update commands.py * Update commands.py * Update commands.py * Update commands.py * Update commands.py * Update commands.py * more verbose copy script * use ibllib @master * Update transfer_experiments.py * MD5 -> BLAKE2B * Update commands.py * Update transfer_experiments.py * Update wizard.py * Update wizard.py * Update wizard.py * add dud detection & update changelog * prevent windows from going to sleep * add doc-strings and type-hints * add docstrings for AdvancedCW * refactoring * offer deletion of dud sessions (working) * add user input to transfer CLI * refactoring copiers * use blake2b hashing from iblutil * pip reset --hard? oh my ... * Update pyproject.toml * Update CHANGELOG.md * add control of status LED * disable LEDs on start of iblrig * add control for LED * updated installation instructions * minor corrections * bug report form * skip initialization of existing singleton * remember state of singleton & GUI position * update icons * correct entry-points and add respective test-case --------- Co-authored-by: olivier <olivier.winter@hotmail.fr>
int-brain-lab · Oct 18, 2023 · 493fc9f · 493fc9f
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml
@@ -0,0 +1,32 @@
+name: Bug Report
+description: File a bug report
+title: "[Bug]: "
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: A bug happened!
+      value: ""
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: What version of IBLRIG are you running?
+      placeholder: 8.x.x
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: shell
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,17 @@ Changelog
 
 -------------------------------
 
+8.11.0
+------
+* add check for availability of internet
+* add proper CLI for data transfer scripts
+* add option for disabling Bpod status LED
+* skip initialization of existing Bpod singleton
+* remember settings for status LED and GUI position
+* move update-check to separate thread
+* detect dud (less than 42 trials) and offer deletion
+* various small bugfixes
+
 8.10.2
 ------
 * hot-fix parsing of path args in transfer_data

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -10,7 +10,7 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ['sphinx_lesson']
+extensions = ['sphinx_lesson', 'sphinx.ext.autosectionlabel']
 source_suffix = ['.rst', '.md']
 
 templates_path = ['_templates']

diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -23,18 +23,11 @@ If your rig is acting up:
 *  Don't hesitate to **contact our developer team** for assistance. We're committed to getting your system back on track.
 
 
-Bug Alert!
-==========
+Bug Reports & Feature Requests
+==============================
 
-Indeed, bugs are persistently present. Our team is in a perpetual quest to eliminate these pesky issues. Your
-contribution is invaluable in this endeavor; kindly consider `creating an issue on GitHub <https://github.com/int-brain-lab/iblrig/issues>`_.
-
-
-Feature Request?
-================
-
-IBLRIG remains in dynamic development, tailored to meet your needs. Your input shapes our direction. `Send us your
-feature-requests via GitHub <https://github.com/int-brain-lab/iblrig/issues>`_ - we will do our best to help you.
+IBLRIG remains in dynamic development. Your input is invaluable in shaping its direction. `Send us your
+bug reports and feature-requests via GitHub <https://github.com/int-brain-lab/iblrig/issues>`_ - we will do our best to help you.
 
 
 Sound Issues
@@ -55,7 +48,7 @@ Screen Issues
 =============
 
 *  The ribbon cable attaching the screen to the driver board is notoriously finicky. If you are having brightness issues or do not have a signal, try gently repositioning this cable and ensure it is tightly seated in its connection.
-*  Screen and ribbon cable can be easily damaged. It is useful to have backup at on hand.
+*  Screen and ribbon cable can be easily damaged. It is useful to have backup at hand.
 *  If the Bonsai display is appearing on the PC screen when a task starts, try unplugging the rig screen, rebooting and plugging the screen back in. Other variations of screen unplugging and rebooting may also work.
    Also make sure, that the ``DISPLAY_IDX`` value in ``hardware_settings.yaml`` is set correctly.
 *  Screen flashing can occur if the power supply does not match the screen specifications. Use a 12V adapter with at least 1A.

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -3,51 +3,85 @@ Installation guide
 
 .. prerequisites::
 
-   *  Windows OS
-   *  git installation.
-   *  Recommended: Notepad++ or a decent text file editor
+   *  A computer running Windows 10 or 11,
+   *  A working installation of `git for windows <https://gitforwindows.org>`_, and
+   *  `Notepad++ <https://notepad-plus-plus.org>`_ or some other decent text editor.
 
+.. tip::
+
+   iblrigv8 can be installed alongside older versions of iblrig without affecting the latter.
+
+.. tip::
+
+   If you believe this guide is incomplete or requires improvements, please don't hesitate to reach out and
+   :ref:`submit a bug report<Bug Reports & Feature Requests>`.
 
-Install Python 3.10
--------------------
 
-Open an Administrator: Windows Powershell prompt and run the following:
+Prepare Windows PowerShell
+--------------------------
+
+Open Windows PowerShell in administrator mode:
+
+* Click on the Windows Start button or press the Windows key on your keyboard.
+* Type "PowerShell" into the search bar.
+* You should see "Windows PowerShell" or "PowerShell" in the search results.
+* Right-click on it.
+* In the context menu that appears, select "Run as administrator."
+
+Now, run the following command at the prompt of Windows PowerShell:
 
 .. code-block:: powershell
 
    Set-ExecutionPolicy RemoteSigned
 
-Then exit the admin window and open a new Windows Powershell prompt (no admin mode) and run the following:
+.. warning:: Make sure you exit the Administrator PowerShell before continuing with the next steps!
+
+.. admonition:: Background
+   :class: seealso
+
+   In PowerShell, there are execution policies that determine the level of security for running scripts. The default execution
+   policy is often set to ``Restricted``, which means that scripts are not allowed to run. However, to install Python or run
+   certain scripts, you need to adjust the execution policy. By setting the execution policy to ``RemoteSigned``, you are
+   allowing the execution of locally created scripts without any digital signature while requiring that remotely downloaded
+   scripts (from the internet) must be digitally signed by a trusted source to run. This strikes a balance between security
+   and usability.
+
+
+Install Python 3.10
+-------------------
+
+Open a `new` Windows Powershell prompt (no administrator mode) and run the following:
 
 .. code-block:: powershell
 
    New-Item -ItemType Directory -Force -Path C:\Temp
    Invoke-WebRequest -Uri https://www.python.org/ftp/python/3.10.11/python-3.10.11-amd64.exe -OutFile C:\Temp\python-3.10.11-amd64.exe
    Start-Process -NoNewWindow -Wait -FilePath C:\Temp\python-3.10.11-amd64.exe -ArgumentList "/passive", "InstallAllUsers=0", "Include_launcher=0", "Include_test=0"
 
+Check that everything worked by running the following command:
 
-.. exercise:: You can check that everything worked by running the following command:
+.. code-block:: powershell
 
-   .. code-block:: powershell
+   C:\Users\IBLuser\AppData\Local\Programs\Python\Python310\.\python.exe --version
 
-      C:\Users\IBLuser\AppData\Local\Programs\Python\Python310\.\python.exe --version
+The command should return ``Python 3.10.11``
 
-   Should return `Python 3.10.11`
 
-.. warning:: Make sure you exit the Administrator Powershell prompt before going to the next steps.
+.. admonition:: Background
+   :class: seealso
+
+   These commands will create a temporary directory, download the Python installer from a specific URL, and then execute the
+   installer with specific installation options, all in a controlled and automated manner.
 
 
 Install iblrigv8
 ----------------
 
-1. From the Powershell command line, clone iblrig to the ‘iblrigv8’ directory, and switch to iblrigv8 branch
+1. From the Powershell command line, clone the `iblrigv8` branch of iblrig to ``C:\iblrigv8``:
 
    .. code-block:: powershell
 
-      cd C:\
-      git clone https://github.com/int-brain-lab/iblrig.git iblrigv8
-      cd iblrigv8
-      git checkout iblrigv8
+      git clone -b iblrigv8 https://github.com/int-brain-lab/iblrig.git C:\iblrigv8
 
 
 2. Install a new virtual environment and update pip (modify the <Username> value if needed)

diff --git a/iblrig/__init__.py b/iblrig/__init__.py
@@ -4,7 +4,7 @@
 # 3) Check CI and eventually wet lab test
 # 4) Pull request to iblrigv8
 # 5) git tag the release in accordance to the version number below (after merge!)
-__version__ = '8.10.2'
+__version__ = '8.10.3'
 
 # The following method call will try to get post-release information (i.e. the number of commits since the last tagged
 # release corresponding to the one above), plus information about the state of the local repository (dirty/broken)

diff --git a/iblrig/base_choice_world_params.yaml b/iblrig/base_choice_world_params.yaml
@@ -8,7 +8,7 @@
 'BONSAI_EDITOR': false
 'CALIBRATION_VALUE': 0.067
 'CONTRAST_SET': [1.0, 0.25, 0.125, 0.0625, 0.0]
-'CONTRAST_SET_PROBABILITY_TYPE': uniform  # uniform, skew_zero
+'CONTRAST_SET_PROBABILITY_TYPE': uniform  # uniform or skew_zero: uniform makes the 0 contrast as likely as the others, while skew_zero makes it half as likely as other contrasts
 'GO_TONE_AMPLITUDE': 0.0272
 'GO_TONE_DURATION': 0.11
 'GO_TONE_IDX': 2

diff --git a/iblrig/base_tasks.py b/iblrig/base_tasks.py
@@ -669,6 +669,7 @@ def start_mixin_bpod(self):
                              "provide a valid port name.")
         self.bpod = Bpod(self.hardware_settings['device_bpod']['COM_BPOD'])
         self.bpod.define_rotary_encoder_actions()
+        self.bpod.set_status_led(False)
 
         def softcode_handler(code):
             """

diff --git a/iblrig/choiceworld.py b/iblrig/choiceworld.py
@@ -38,7 +38,7 @@ def compute_adaptive_reward_volume(subject_weight_g, reward_volume_ul, delivered
 
 def get_subject_training_info(
         subject_name, task_name='_iblrig_tasks_trainingChoiceWorld',
-        default_reward=DEFAULT_REWARD_VOLUME, mode='silent', **kwargs):
+        default_reward=DEFAULT_REWARD_VOLUME, mode='silent', **kwargs) -> tuple[int, float, dict]:
     """
     Goes through the history of a subject and gets the latest
     training phase and the adaptive reward volume for this subject