Fix latex, RST warnings

Author: meson800

build.py

@@ -171,7 +171,7 @@ def summarize_latex_logfile(logs):
     if args.parallel or args.emit_gh_annotations:
         html_args.insert(3, '--no-color')
     latex_env = os.environ.copy()
-    latex_env["LATEXMKOPTS"] = "-interaction=batchmode"
+    latex_env["LATEXMKOPTS"] = "-interaction=nonstopmode"
 
     gh_annotations = []
 

docs/conf.py

@@ -190,6 +190,8 @@
 
 def setup(app):
     from sphinx.util.texescape import tex_replacements
+    tex_replacements.append(('≤', r'\(\leq\)'))
+    tex_replacements.append(('≥', r'\(\geq\)'))
     tex_replacements.append(('μ', r'\(\mu\)'))
     tex_replacements.append(('°', r'\(^\circ\)'))
     tex_replacements.append(('℃', r'\(^\circ\)C'))

docs/instruments/core_facilities/Koch_flow.rst

@@ -72,12 +72,12 @@ Training Details
      * If you need to do a longer sort for an experiment, you could sign up for the 1-hour assisted use, then separately sign up for more time immediately after to finish your sort.
 
 Sony MA-900
------------
+===========
 
 The Sony MA900 cell sorter has a `SOP <https://docs.google.com/document/d/1toqMY_qnDy0_YDkcEr2ktDJWcteKe0Pj42_scukqT5s/edit>`__ that you can follow for startup and shutdown.
 
 Startup
-^^^^^^^
+~~~~~~~
 
 You only need to start up the Sony if you want to use it over the weekend, on holidays, or outside of normal hours.
 During the week, core staff will do the start up in the morning.
@@ -121,7 +121,7 @@ The Sony is generally very easy to startup once you've seen how to; you mostly f
      * You don’t need to include startup time when signing up to sort on weekends/holidays (e.g. don’t pay for startup time).
 
 Sample Prep and Sorting
-^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~
 
 1. Get ice. Keep your samples on ice as much as possible after dissociation.
 2. Dissociate cells using appropriate method. Centrifuge the cells to pellet them.
@@ -236,7 +236,7 @@ Sample Prep and Sorting
     6. Add on extra time for setting up the workspace, setting voltages and gates, swapping samples, the final Bleach Cleaning and DI Rinse steps, and exporting your data.
 
 Shutdown
-^^^^^^^^
+~~~~~~~~
 
 Follow the shutdown SOP, with the exception that on step 7 ("Turn off the air compressor and blue switch on the air-line"), 
 do **not** turn off the blue switch on the air-line, 

docs/protocols/tc/virus/viral_titer.rst

@@ -98,7 +98,7 @@ Note that individual cells with detectable expression may be contain one or more
 
 First, let's define the **multiplicity of infection (MOI)**, :math:`\lambda`, as the ratio of viral transducing units (TU) to number of cells, *n*:
 
-.. math:: \lambda = \frac{\text{# TU}}{n}
+.. math:: \lambda = \frac{\text{number of TU}}{n}
 
 We can obtain a particular MOI in an experiment by using a calculated **volume of virus**, *v*, if we know the **viral titer**, *t*:
 
@@ -122,12 +122,10 @@ However, it is difficult to quantify the exact number of transductions in indivi
 cells with at least one transduction:
 
 .. math::
-  \begin{align}
     P(x>0) &= 1 - P(x=0) \\
     &= 1 - \frac{\lambda^0 e^{-\lambda}}{0!} \\
     &= 1 - e^{-\lambda} \\
     &= 1 - e^{v / n \ \times \ t}
-  \end{align}
 
 Thus, the flow cytometry data from the experiment above can give us a fraction of expressing cells, which we can use with known values of *v* and *n* (experimental parameters)
 to find *t*, the viral titer. To make this calculation more accurate, we can measure the fraction of expressing cells for several different volumes of virus---exactly the 

docs/training/onboarding/day_0_setup.rst

@@ -50,10 +50,12 @@ EHS system and add all necessary trainings to your profile.
 .. note::
    To complete the Signature: Read Dept. Chemical Hygiene Plan training, please read the Chemical Hygiene Plan and then sign the attestation form.
    The attestation form is available at:
-    https://web-cert.mit.edu/cheme/resources/lab/ehs/ehs_cert.html
-    You will need an MIT web certificate to access and complete the form.
-    If you do not yet have a web certificate, you can obtain one here:
-      https://ist.mit.edu/mit-apps/certaid
+   https://web-cert.mit.edu/cheme/resources/lab/ehs/ehs_cert.html
+
+   MIT certificates were phased out in summer 2026. There will be some new method to do this.
+
+   In the past, you had to get a web certificate from:
+   https://ist.mit.edu/mit-apps/certaid
 
 1. If you are going to be helping with mouse work, still under the
    'My Profile' tab, you should click **Join Another Group** under training
@@ -295,140 +297,63 @@ Coding and collaboration
   and select the 64-bit installer for your OS.
 
   When installing, select **Add Python to PATH**; this ensures that when you type ``python`` at a terminal, you get this version you
-  just installed. Other software can also access this "default" installation.
+  just installed. Other software can also access this "default" installation. After installing, restart VS Code.
+
+  .. admonition:: What is PATH?
+
+    ``PATH`` is a "environment variable", e.g. something that any program running
+    in the "environment" of your computer can access. It is a list of folders where software can be found.
+    In a command line, when you type a program name (like ``ls``, or ``python``, or ``git``)
+    without specifying where the program is, your computer iterates through every folder in ``PATH`` to see
+    if it can find the program there.
+
+    Bonus fact: virtual environments work by temporarily messing with ``PATH``, redirecting e.g. Python to
+    the virtual environment install.
 
   .. admonition:: Fixing Python “command not found” (Windows & macOS)
    :class: warning
-
-   This protocol addresses a common issue where Python is installed correctly,
-   but typing ``python`` or ``pip`` in a terminal results in an error such as:
+   
+   If you see errors like
 
    - ``'python' is not recognized as an internal or external command``
    - ``command not found: python``
 
-   The most common cause is that Python exists on disk, but its directory
-   is missing from the PATH environment variable.
-
-   Windows (Command Prompt / PowerShell)
-   ------------------------------------------------------------
-
-   Confirm that Python is installed
-   --------------------------------
-
-   1. Open **PowerShell**
-   2. Navigate to the Python installation directory, for example::
-
-         C:\Users\<USERNAME>\AppData\Local\Python\pythoncore-3.14-64\
-
-   3. In PowerShell, run Python directly using the call operator ``&``::
-
-         & "C:\Users\<USERNAME>\AppData\Local\Python\pythoncore-3.14-64\python.exe" --version
-
-   If a Python version is printed, Python is installed correctly and the issue
-   is related to PATH configuration.
-
-   ------------------------------------------------------------
-   Fix PATH using the Environment Variables GUI (recommended)
-   ------------------------------------------------------------
-
-   **Do not use ``setx PATH``**, as it can truncate PATH and break other software.
-
-   1. Press the **Windows key**
-   2. Search for **Edit environment variables**
-   3. Open **Edit the system environment variables**
-   4. Click **Environment Variables…**
-
-   You will see two sections:
-   - **User variables for <USERNAME>** (top box)
-   - **System variables** (bottom box)
-
-   5. In the **User variables** section, select **Path**
-   6. Click **Edit…**
-
-   You will now see a list of directories that make up your PATH.
-
-   7. Click **New**
-   8. Add::
-
-         C:\Users\<USERNAME>\AppData\Local\Python\pythoncore-3.14-64\
-
-   9. Click **New** again
-   10. Add::
-
-         C:\Users\<USERNAME>\AppData\Local\Python\pythoncore-3.14-64\Scripts\
-
-   11. Click **OK** to close the Path editor
-   12. Click **OK** to close the Environment Variables window
-
-   **Important:** Close all open PowerShell and Command Prompt windows,
-   then open a new terminal.
-
-   Verify the fix::
-
-      python --version
-      pip --version
-      where.exe python
-      where.exe pip
-
-   If ``where.exe python`` points to the ``pythoncore`` directory, PATH is fixed.
-
-   Common Windows pitfalls
-   ------------------------------------------------------------
-
-   PowerShell vs Command Prompt
-   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   - PowerShell requires ``&`` to execute a quoted executable path
-   - Command Prompt does not
-
-   App execution aliases
-   ~~~~~~~~~~~~~~~~~~~~~
-   Windows may redirect ``python`` to the Microsoft Store.
-
-   To disable this:
-   1. Open the Start menu
-   2. Search for **App execution aliases**
-   3. Turn **OFF** ``python.exe`` and ``python3.exe``
-
-   macOS (differences from Windows)
-   ------------------------------------------------------------
-
-   On macOS, PATH issues are handled through shell configuration files,
-   not a graphical environment variables editor.
-
-   Check Python::
+   then you likely forgot do the above step (clicking Add Python to PATH),
+   or you didn't restart VS Code.
 
-      which python3
-      python3 --version
+   The easiest remediation is simply uninstall Python and reinstall it, while
+   clicking the box.
 
-   Fix PATH (zsh default):
+   If you don't want to do that for some reason, you can manually add Python to PATH. 
 
-   1. Edit your shell configuration file::
+   **Windows**
 
-         nano ~/.zshrc
+   You need to find where Python is installed. This will vary! The easiest way to do this
+   is just search for ``python.exe`` to locate where that folder is. Say that the location is
 
-   2. Add (example for Homebrew)::
+    ``C:\Users\<USERNAME>\AppData\Local\Python\python-3.14\python.exe``
 
-         export PATH="/opt/homebrew/bin:$PATH"
+   Then:
 
-   3. Reload::
+   1. Press the Windows key on your keyboard to bring up the search.
+   2. Search for *Edit environment variables*
+   3. In the box that shows up, hit *Edit the system environment variables*.
+   4. Click *Environment Variables*.
+   5. In the **User variables for <USERNAME>** box, find the **Path** variable and hit Edit.
+   6. In the list of directories that shows up, hit **New** and add the folder containing Python
+      identified earlier.
+   7. Hit OK in the boxes and **restart any open terminals and VSCode to pick up the change**. The most
+      reliable method here is logging out and logging back in.
 
-         source ~/.zshrc
+   **macOS / Linux**
 
-   Verify::
+   On macOS and Linux, you handle path by editing your shell configuration file, normally either
+   at ``~/.zshrc`` for zsh or ``~/.bashrc`` for Bash.
 
-      python3 --version
-      pip3 --version
+   In these lines, you should add an export call to add the Python location to the end of path, like:
 
-   Key takeaways
-   ------------------------------------------------------------
 
-   - Python is often installed correctly, but missing from PATH
-   - On Windows:
-     - Edit the existing **Path** variable
-     - Do not create new variables
-     - Avoid ``setx PATH``
-   - On macOS:
-     - PATH is managed in ``~/.zshrc`` or ``~/.bashrc``
+   ``export PATH="$PATH:/path/to/python/that/you/found``
 
   .. admonition:: On snakes and Anaconda