add tips and some other env files

nmfs-opensci · Jun 1, 2024 · 72de23a · 72de23a
1 parent 96b2d83
commit 72de23a
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diff --git a/_quarto.yml b/_quarto.yml
@@ -42,6 +42,8 @@ website:
         href: posts/Set-up-centos-security.Rmd
       - text: "Set-up authentication"
         href: posts/set-up-authentication.Rmd
+      - text: "Tips"
+        href: posts/tips.Rmd
 
 format:
   html:

diff --git a/ci/VAST/Dockerfile b/ci/VAST/Dockerfile
@@ -0,0 +1,19 @@
+# geospatial rocker
+FROM openscapes/rocker:a7596b5
+
+USER ${NB_USER}
+
+WORKDIR ${HOME}
+
+# fix security bug
+# https://github.com/jupyterhub/jupyter-server-proxy/security/advisories/GHSA-w3vc-fx9p-wp4v
+RUN pip install jupyter-server-proxy>=3.2.3 --no-deps
+
+# By default, the versioned rocker image (which openscapes/rocker uses) will use 
+# the Posit repository which has binaries for Unbuntu (which rocker image uses)
+
+# VAST dependencies packages
+RUN R -e 'install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)'
+RUN R -e 'install.packages("TMB")'
+RUN R -e 'devtools::install_github("james-thorson/FishStatsUtils@main", INSTALL_opts="--no-staged-install")'
+RUN R -e 'devtools::install_github("james-thorson/VAST@main", INSTALL_opts="--no-staged-install")'
diff --git a/ci/iopython-tf/Dockerfile b/ci/iopython-tf/Dockerfile
@@ -1,4 +1,4 @@
-FROM openscapes/python:f577786
+FROM openscapes/python:0100a87
 
 # install additional package...
 

diff --git a/ci/iopython/Dockerfile b/ci/iopython/Dockerfile
@@ -1,4 +1,4 @@
-FROM openscapes/python:f577786
+FROM openscapes/python:0100a87
 
 # install additional package...
 

diff --git a/ci/iopython/instructions.md b/ci/iopython/instructions.md
@@ -28,7 +28,7 @@ cd ci/iopython
 ```
 2. Update the docker tag to the date.
 ```
-DOCKER_TAG="20230901"
+DOCKER_TAG="20240409"
 ```
 2. Build the image. `.` means current directory. `eeholmes/iopython` is the name of the repo on DockerHub. See notes below. 
 ```

diff --git a/ci/iorocker/Dockerfile b/ci/iorocker/Dockerfile
@@ -1,13 +1,18 @@
 FROM openscapes/rocker:a7596b5
 # tell RStudio the right path so it is in the conda environment
-RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
+USER root
+RUN echo "PATH=${PATH}" >> "${R_HOME}/etc/Renviron.site"
 
 # install additional package...
 
 USER ${NB_USER}
 
 WORKDIR ${HOME}
 
+# fix security bug
+# https://github.com/jupyterhub/jupyter-server-proxy/security/advisories/GHSA-w3vc-fx9p-wp4v
+RUN pip install jupyter-server-proxy>=3.2.3 --no-deps
+
 # By default, the versioned rocker image (which openscapes/rocker uses) will use 
 # the Posit repository which has binaries for Unbuntu (which rocker image uses)
 

diff --git a/ci/py-rocker-base/environment.yml b/ci/py-rocker-base/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.10
-  - jupyter-server-proxy
+  - jupyter-server-proxy>=4.1.1
   - jupyterlab>4
   - jupyterlab-myst
   - jupyterhub-singleuser

diff --git a/docs/posts/JHub-User-Guide.html b/docs/posts/JHub-User-Guide.html
@@ -159,6 +159,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/Set-up-centos-security.html b/docs/posts/Set-up-centos-security.html
@@ -193,6 +193,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/Set-up-centos-tljh.html b/docs/posts/Set-up-centos-tljh.html
@@ -191,6 +191,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/Set-up-centos.html b/docs/posts/Set-up-centos.html
@@ -193,6 +193,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/Set-up-daskhub.html b/docs/posts/Set-up-daskhub.html
@@ -159,6 +159,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/Setup-Notes.html b/docs/posts/Setup-Notes.html
@@ -156,6 +156,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/set-up-authentication.html b/docs/posts/set-up-authentication.html
@@ -30,6 +30,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href="../posts/tips.html" rel="next">
 <link href="../posts/Set-up-centos-security.html" rel="prev">
 <link href="../images/nmfs-opensci-logo2-notext.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
@@ -158,6 +159,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>
@@ -821,6 +828,9 @@ <h3 class="anchored" data-anchor-id="if-you-use-daskhub-helm-chart">If you use d
       </a>          
   </div>
   <div class="nav-page nav-page-next">
+      <a href="../posts/tips.html" class="pagination-link" aria-label="Tips">
+        <span class="nav-page-text">Tips</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
   </div>
 </nav>
 </div> <!-- /content -->

diff --git a/docs/posts/set-up-jh-aws.html b/docs/posts/set-up-jh-aws.html
@@ -159,6 +159,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/set-up-jh-gcp.html b/docs/posts/set-up-jh-gcp.html
@@ -159,6 +159,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>

diff --git a/docs/posts/set-up-vm.html b/docs/posts/set-up-vm.html
@@ -157,6 +157,12 @@
   <a href="../posts/set-up-authentication.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Set-up authentication</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../posts/tips.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tips</span></a>
+  </div>
 </li>
     </ul>
     </div>