deploy updates

sagemathinc · Jan 6, 2025 · 0003422 · 0003422
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c8453c57e666c26f115a815e1d6a4c64
+config: daadc21f67da77ea601bd3f8a4a9518f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/R_IDE.html b/R_IDE.html
@@ -213,7 +213,7 @@ <h2>Other Ways<a class="headerlink" href="#other-ways" title="Link to this headi
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/_downloads/0444300746ad21e7ad7eaa3d6fb85332/environment.yml b/_downloads/0444300746ad21e7ad7eaa3d6fb85332/environment.yml
@@ -0,0 +1,11 @@
+name: myenv
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - ipykernel
+  - pandas
+  - matplotlib
+  - biopython
+  - samtools
diff --git a/_sources/howto/custom-jupyter-kernel.rst.txt b/_sources/howto/custom-jupyter-kernel.rst.txt
@@ -17,7 +17,7 @@ These instructions are for the case in which you want to create a Jupyter kernel
 
 1. If you haven't already, create your own Python environment:
 
-- Python via `venv`_ (for demo purposes, we install an old version of NumPy)::
+- Python via `venv`_ (for demo purposes, we install an old version of NumPy. Make sure to install ``ipykernel`` as well)::
 
     ~$ mkdir myenv
     ~$ cd myenv/
@@ -34,13 +34,20 @@ These instructions are for the case in which you want to create a Jupyter kernel
     >>> np.__version__
     '1.26.4'
 
-- Anaconda (make sure to also install ``ipykernel`` via the environment.yml configuration)::
+- Anaconda:
 
-    ~$ anaconda2023
-    (base) ~$ mamba env create --prefix ~/myenv --file=environment.yml
-    (base) ~$ conda activate ~/myenv
-    (/home/user/myenv) ~$ python
-    [...]
+  * First start the root anaconda environment using ``anaconda``.
+  * Then create a new environment **with a prefix** (important!).
+  * Install ``ipykernel`` along your other packages in the ``environment.yml`` configuration (:download:`example environment.yml <../_files/environment.yml>`).
+  * Later, you can do ``source ~/myenv/bin/activate`` directly.
+
+  ::
+
+      ~$ anaconda
+      (base) ~$ mamba env create --prefix ~/myenv --file=environment.yml
+      (base) ~$ conda activate ~/myenv
+      (/home/user/myenv) ~$ python
+      [...]
 
 .. note::
 

diff --git a/_sources/howto/install-python-lib.rst.txt b/_sources/howto/install-python-lib.rst.txt
@@ -227,9 +227,9 @@ To get it installed in Anaconda as a user, do this:
 
 1. Open a terminal.
 
-2. Type ``anaconda2023`` (or just ``anaconda`` to launch the newest version)
+2. Type ``anaconda`` to launch.
 
-3. Type ``mamba env create --prefix ~/myenv -c mro r`` This creates a new isolated local (hence ``--prefix ...``) environment in the directory ``~/myenv`` with the package "r" as its source coming from the channel "mro" (Microsoft's Open R). Instead of that, you can add any other anaconda package or use ``--file=environment.yml`` to reconstruct from a full environment definition. For more details, see http://conda.pydata.org/docs/using/envs.html#create-an-environment.
+3. Type ``mamba env create --prefix ~/myenv --file=environment.yml`` This creates a new isolated local (hence ``--prefix ...``) environment in the directory ``~/myenv``. Use an :download:`environment.yml <../_files/environment.yml>` to reconstruct from a full definition. For more details, see http://conda.pydata.org/docs/using/envs.html#create-an-environment.
 
 4. When installing, it will resolve the package dependencies, download packages, unpack and install them. Afterwards, run ``mamba clean --all --yes`` to save disk space.
 

diff --git a/_sources/latex-features.rst.txt b/_sources/latex-features.rst.txt
@@ -109,7 +109,7 @@ You could also use GNU Makefiles and call ``make ...;`` from here.
 
 **Default build command**
 
-The selected build command is stored in a companion file in the project.
+The selected build command is stored in a companion file in the project, namely ``*.tex.syncdb``.
 You can also store the default engine or even hardcode the build command in the LaTeX document itself.
 There are two relevant directives, which are special comment lines at the beginning of your file.
 

diff --git a/_sources/latex-start.rst.txt b/_sources/latex-start.rst.txt
@@ -45,7 +45,7 @@ To use the LaTeX editor, open or create a file whose name ends in ``.tex``. By d
 
 * The **Build Control** view gives you more control over how the compilation process works:
 
-  * You can click in the build command line and edit it however you want, or select a different engine from the dropdown menu.
+  * You can click in the :ref:`build command <latex-build-engine>` line and edit it however you want, or select a different engine from the dropdown menu.
     By default, we compile using `LatexMK`_, which manages temporary files and BibTeX.
 
   * Click **Clean** to delete autogenerated temporary files.

diff --git a/account-dropdown.html b/account-dropdown.html
@@ -188,7 +188,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account-toolbar.html b/account-toolbar.html
@@ -275,7 +275,7 @@ <h3><a class="toc-backref" href="#id12" role="doc-backlink">Upgrades</a><a class
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/licenses.html b/account/licenses.html
@@ -237,7 +237,7 @@ <h4>Dedicated RAM<a class="headerlink" href="#dedicated-ram" title="Link to this
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/preferences.html b/account/preferences.html
@@ -281,7 +281,7 @@ <h2><a class="toc-backref" href="#id13" role="doc-backlink">Terminal settings</a
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/public-files.html b/account/public-files.html
@@ -151,7 +151,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/purchases.html b/account/purchases.html
@@ -274,7 +274,7 @@ <h2><a class="toc-backref" href="#id13" role="doc-backlink">API v2 endpoint</a><
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/ssh.html b/account/ssh.html
@@ -177,7 +177,7 @@ <h2>Display local public key fingerprints<a class="headerlink" href="#display-lo
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/account/support.html b/account/support.html
@@ -152,7 +152,7 @@ <h2>Support tickets<a class="headerlink" href="#support-tickets" title="Link to
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/activity-bar.html b/activity-bar.html
@@ -198,7 +198,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/ai.html b/ai.html
@@ -294,7 +294,7 @@ <h2>Typeset Scientific Content with LaTeX<a class="headerlink" href="#typeset-sc
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/alternativeto/index.html b/alternativeto/index.html
@@ -168,7 +168,7 @@ <h1>Comparing with Others<a class="headerlink" href="#comparing-with-others" tit
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/alternativeto/jupyterhub.html b/alternativeto/jupyterhub.html
@@ -200,7 +200,7 @@ <h2>Reliability<a class="headerlink" href="#reliability" title="Link to this hea
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api-examples.html b/api-examples.html
@@ -296,7 +296,7 @@ <h2>IFrame communication<a class="headerlink" href="#iframe-communication" title
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/add_collaborator.html b/api/add_collaborator.html
@@ -243,7 +243,7 @@ <h1>add_collaborator<a class="headerlink" href="#add-collaborator" title="Link t
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/add_license_to_project.html b/api/add_license_to_project.html
@@ -225,7 +225,7 @@ <h1>add_license_to_project<a class="headerlink" href="#add-license-to-project" t
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/change_email_address.html b/api/change_email_address.html
@@ -249,7 +249,7 @@ <h1>change_email_address<a class="headerlink" href="#change-email-address" title
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/change_password.html b/api/change_password.html
@@ -233,7 +233,7 @@ <h1>change_password<a class="headerlink" href="#change-password" title="Link to
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/copy_path_between_projects.html b/api/copy_path_between_projects.html
@@ -284,7 +284,7 @@ <h1>copy_path_between_projects<a class="headerlink" href="#copy-path-between-pro
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/copy_path_delete.html b/api/copy_path_delete.html
@@ -223,7 +223,7 @@ <h1>copy_path_delete<a class="headerlink" href="#copy-path-delete" title="Link t
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/copy_path_status.html b/api/copy_path_status.html
@@ -243,7 +243,7 @@ <h1>copy_path_status<a class="headerlink" href="#copy-path-status" title="Link t
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/copy_public_path_between_projects.html b/api/copy_public_path_between_projects.html
@@ -251,7 +251,7 @@ <h1>copy_public_path_between_projects<a class="headerlink" href="#copy-public-pa
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/create_account.html b/api/create_account.html
@@ -250,7 +250,7 @@ <h1>create_account<a class="headerlink" href="#create-account" title="Link to th
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/create_project.html b/api/create_project.html
@@ -235,7 +235,7 @@ <h1>create_project<a class="headerlink" href="#create-project" title="Link to th
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/create_support_ticket.html b/api/create_support_ticket.html
@@ -277,7 +277,7 @@ <h1>create_support_ticket<a class="headerlink" href="#create-support-ticket" tit
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/delete_account.html b/api/delete_account.html
@@ -232,7 +232,7 @@ <h1>delete_account<a class="headerlink" href="#delete-account" title="Link to th
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/disconnect_from_project.html b/api/disconnect_from_project.html
@@ -221,7 +221,7 @@ <h1>disconnect_from_project<a class="headerlink" href="#disconnect-from-project"
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/forgot_password.html b/api/forgot_password.html
@@ -231,7 +231,7 @@ <h1>forgot_password<a class="headerlink" href="#forgot-password" title="Link to
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/get_available_upgrades.html b/api/get_available_upgrades.html
@@ -250,7 +250,7 @@ <h1>get_available_upgrades<a class="headerlink" href="#get-available-upgrades" t
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/get_support_tickets.html b/api/get_support_tickets.html
@@ -243,7 +243,7 @@ <h1>get_support_tickets<a class="headerlink" href="#get-support-tickets" title="
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/get_usernames.html b/api/get_usernames.html
@@ -233,7 +233,7 @@ <h1>get_usernames<a class="headerlink" href="#get-usernames" title="Link to this
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/index.html b/api/index.html
@@ -482,7 +482,7 @@ <h2>IFrame communication<a class="headerlink" href="#iframe-communication" title
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/index0.html b/api/index0.html
@@ -194,7 +194,7 @@ <h1>API Message Reference<a class="headerlink" href="#api-message-reference" tit
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/invite_collaborator.html b/api/invite_collaborator.html
@@ -239,7 +239,7 @@ <h1>invite_collaborator<a class="headerlink" href="#invite-collaborator" title="
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
 
 

diff --git a/api/invite_noncloud_collaborators.html b/api/invite_noncloud_collaborators.html
@@ -265,7 +265,7 @@ <h1>invite_noncloud_collaborators<a class="headerlink" href="#invite-noncloud-co
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+    <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
   </div>
-Original file line number
+Diff line change
@@ Expand Up @@
       <hr/>
       <div role="contentinfo">
-        <p>&#169; Copyright 2024, Sagemath, Inc., CC BY-4.0 licensed.</p>
+        <p>&#169; Copyright 2025, Sagemath, Inc., CC BY-4.0 licensed.</p>
       </div>
@@ Expand Down @@