Merge pull request #95 from malariagen/GH94_remove_Colab_links

Remove Colab and Binder menu options. Remove old environment.yml file. Use mgenv v6.0.6 in notebooks.
malariagen · Nov 26, 2024 · a59c0b0 · a59c0b0
2 parents f063ad2 + a4ccf82
commit a59c0b0
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Showing 28 changed files with 6,825 additions and 6,541 deletions.
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -10,7 +10,8 @@ repository:
   branch: master
 launch_buttons:
   notebook_interface: "jupyterlab"
-  colab_url: "https://colab.research.google.com"
+  colab_url: ""
+  binderhub_url: ""
 html:
   use_repository_button : true
   use_issues_button: true

diff --git a/docs/af1/af1.0.ipynb b/docs/af1/af1.0.ipynb
@@ -1244,9 +1244,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-binder-5.0.0",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-binder-5.0.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1258,7 +1258,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/af1/af1.1.ipynb b/docs/af1/af1.1.ipynb
@@ -1264,9 +1264,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-binder-5.0.0",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-binder-5.0.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1278,7 +1278,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/af1/af1.2.ipynb b/docs/af1/af1.2.ipynb
@@ -693,9 +693,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-binder-5.0.0",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-binder-5.0.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -707,7 +707,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/af1/af1.3.ipynb b/docs/af1/af1.3.ipynb
@@ -656,9 +656,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-binder-5.0.0",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-binder-5.0.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -670,7 +670,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/af1/af1.4.ipynb b/docs/af1/af1.4.ipynb
@@ -693,9 +693,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-mgenv-5.1.0",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-mgenv-5.1.0-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -707,7 +707,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/af1/cloud.ipynb b/docs/af1/cloud.ipynb
diff --git a/docs/af1/download.ipynb b/docs/af1/download.ipynb
@@ -800,9 +800,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -814,7 +814,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.0.ipynb b/docs/ag3/ag3.0.ipynb
@@ -1410,9 +1410,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1424,7 +1424,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.1.ipynb b/docs/ag3/ag3.1.ipynb
@@ -662,9 +662,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -676,7 +676,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.10.ipynb b/docs/ag3/ag3.10.ipynb
@@ -1036,9 +1036,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-mgenv-6.0.5",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-mgenv-6.0.5-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1050,7 +1050,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.11.ipynb b/docs/ag3/ag3.11.ipynb
@@ -720,9 +720,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-mgenv-6.0.5",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-mgenv-6.0.5-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -734,7 +734,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.12.ipynb b/docs/ag3/ag3.12.ipynb
@@ -679,9 +679,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-mgenv-6.0.5",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-mgenv-6.0.5-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -693,7 +693,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.13.ipynb b/docs/ag3/ag3.13.ipynb
@@ -660,9 +660,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "global-global-mgenv-6.0.5",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "conda-env-global-global-mgenv-6.0.5-py"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -674,7 +674,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.2.ipynb b/docs/ag3/ag3.2.ipynb
@@ -750,9 +750,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -764,7 +764,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.4.ipynb b/docs/ag3/ag3.4.ipynb
@@ -726,9 +726,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -740,7 +740,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.5.ipynb b/docs/ag3/ag3.5.ipynb
@@ -782,9 +782,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -796,7 +796,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.6.ipynb b/docs/ag3/ag3.6.ipynb
@@ -778,9 +778,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -792,7 +792,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.7.ipynb b/docs/ag3/ag3.7.ipynb
@@ -949,9 +949,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -963,7 +963,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/ag3/ag3.8.ipynb b/docs/ag3/ag3.8.ipynb
@@ -965,9 +965,9 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "global-global-mgenv-6.0.6",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-global-global-mgenv-6.0.6-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -979,7 +979,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,