Merge pull request #91 from malariagen/83-de-mybinder-ification

De-MyBinder-ification
malariagen · Nov 18, 2024 · f063ad2 · f063ad2
2 parents d9839ee + c9a0513
commit f063ad2
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Showing 20 changed files with 28 additions and 29 deletions.
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -11,7 +11,6 @@ repository:
 launch_buttons:
   notebook_interface: "jupyterlab"
   colab_url: "https://colab.research.google.com"
-  binderhub_url: "https://gke.mybinder.org"
 html:
   use_repository_button : true
   use_issues_button: true

diff --git a/docs/af1/af1.0.ipynb b/docs/af1/af1.0.ipynb
@@ -577,7 +577,7 @@
     "\n",
     "Raw sequence reads, sequence read alignments and SNP calls are available for download from the European Nucleotide Archive (ENA). Further information on how to find and download these data is provided in the [data download guide](https://malariagen.github.io/vector-data/af1/download.html).\n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](https://malariagen.github.io/vector-data/af1/cloud.html)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](https://malariagen.github.io/vector-data/af1/cloud.html)."
    ]
   },
   {

diff --git a/docs/af1/af1.1.ipynb b/docs/af1/af1.1.ipynb
@@ -81,7 +81,7 @@
     "\n",
     "Data from `Af1.1` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/af1/af1.2.ipynb b/docs/af1/af1.2.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "Data from `Af1.2` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/af1/af1.3.ipynb b/docs/af1/af1.3.ipynb
@@ -66,7 +66,7 @@
     "\n",
     "Data from `Af1.3` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/af1/af1.4.ipynb b/docs/af1/af1.4.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "Data from `Af1.4` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.0.ipynb b/docs/ag3/ag3.0.ipynb
@@ -81,7 +81,7 @@
     "\n",
     "Raw sequence reads, sequence read alignments and SNP calls are available for download from the European Nucleotide Archive (ENA). Further information on how to find and download these data is provided in the [data download guide](download).\n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.1.ipynb b/docs/ag3/ag3.1.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "Data from `Ag3.1` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.10.ipynb b/docs/ag3/ag3.10.ipynb
@@ -74,7 +74,7 @@
     "\n",
     "Data from `Ag3.10` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {
@@ -1036,9 +1036,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "developer-developer-training-nb-maintenance-mgen-9.0.0",
+   "display_name": "global-global-mgenv-6.0.5",
    "language": "python",
-   "name": "conda-env-developer-developer-training-nb-maintenance-mgen-9.0.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.5-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1050,7 +1050,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.11.ipynb b/docs/ag3/ag3.11.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "Data from `Ag3.11` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {
@@ -720,9 +720,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "ahernank-ahernank-pug-dev",
+   "display_name": "global-global-mgenv-6.0.5",
    "language": "python",
-   "name": "conda-env-ahernank-ahernank-pug-dev-py"
+   "name": "conda-env-global-global-mgenv-6.0.5-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -734,7 +734,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.12.ipynb b/docs/ag3/ag3.12.ipynb
@@ -69,7 +69,7 @@
     "\n",
     "Data from `Ag3.12` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.13.ipynb b/docs/ag3/ag3.13.ipynb
@@ -69,7 +69,7 @@
     "\n",
     "Data from `Ag3.13` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.2.ipynb b/docs/ag3/ag3.2.ipynb
@@ -80,7 +80,7 @@
     "\n",
     "Data from `Ag3.2` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.3.ipynb b/docs/ag3/ag3.3.ipynb
@@ -73,7 +73,7 @@
     "\n",
     "Data from `Ag3.3` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.4.ipynb b/docs/ag3/ag3.4.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "Data from `Ag3.4` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.5.ipynb b/docs/ag3/ag3.5.ipynb
@@ -71,7 +71,7 @@
     "\n",
     "Data from `Ag3.5` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.6.ipynb b/docs/ag3/ag3.6.ipynb
@@ -72,7 +72,7 @@
     "\n",
     "Data from `Ag3.6` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.7.ipynb b/docs/ag3/ag3.7.ipynb
@@ -75,7 +75,7 @@
     "\n",
     "Data from `Ag3.7` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.8.ipynb b/docs/ag3/ag3.8.ipynb
@@ -75,7 +75,7 @@
     "\n",
     "Data from `Ag3.8` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {

diff --git a/docs/ag3/ag3.9.ipynb b/docs/ag3/ag3.9.ipynb
@@ -79,7 +79,7 @@
     "\n",
     "Data from `Ag3.9` are hosted by several different services. \n",
     "\n",
-    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
    ]
   },
   {
@@ -1507,9 +1507,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "developer-developer-training-nb-maintenance-mgen-8.7.0",
+   "display_name": "global-global-mgenv-6.0.5",
    "language": "python",
-   "name": "conda-env-developer-developer-training-nb-maintenance-mgen-8.7.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.5-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1521,7 +1521,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,