Updated notebooks (#295)

* updated example_restriction (#285) Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> * small fixes (#294) * allow run all on notebooks that have pip install for google colab --------- Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com>
pydna-group · Oct 7, 2024 · 8543b7b · 8543b7b
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diff --git a/docs/notebooks/CRISPR.ipynb b/docs/notebooks/CRISPR.ipynb
@@ -28,9 +28,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {
@@ -54,7 +59,6 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-
    "outputs": [
     {
      "name": "stdout",

diff --git a/docs/notebooks/Dseq.ipynb b/docs/notebooks/Dseq.ipynb
@@ -23,9 +23,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Dseq_Features.ipynb b/docs/notebooks/Dseq_Features.ipynb
@@ -30,9 +30,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Example_CRISPR.ipynb b/docs/notebooks/Example_CRISPR.ipynb
@@ -75,9 +75,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#Install pydna for colab.\n",
-    "%%capture\n",
-    "!pip install git+https://github.com/BjornFJohansson/pydna.git@dev_bjorn"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Example_Gibson.ipynb b/docs/notebooks/Example_Gibson.ipynb
@@ -27,9 +27,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Example_Restriction.ipynb b/docs/notebooks/Example_Restriction.ipynb
diff --git a/docs/notebooks/Gibson.ipynb b/docs/notebooks/Gibson.ipynb
@@ -32,9 +32,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Importing_Seqs.ipynb b/docs/notebooks/Importing_Seqs.ipynb
@@ -34,9 +34,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/PCR.ipynb b/docs/notebooks/PCR.ipynb
@@ -32,9 +32,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {

diff --git a/docs/notebooks/Restrict_Ligate_Cloning.ipynb b/docs/notebooks/Restrict_Ligate_Cloning.ipynb
@@ -29,9 +29,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install pydna \n",
-    "%%capture\n",
-    "!pip install pydna"
+    "# Install pydna (only when running on Colab)\n",
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    %%capture\n",
+    "    # Install the current development version of pydna (comment to install pip version)\n",
+    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
+    "    # Install pip version instead (uncomment to install)\n",
+    "    # !pip install pydna\n"
    ]
   },
   {