neuromatch · iamzoltan · Dec 15, 2023 · Dec 15, 2023 · Dec 15, 2023 · Dec 15, 2023
diff --git a/tutorials/W1D1_Instructions/W1D1_Intro.ipynb b/tutorials/W1D1_Instructions/W1D1_Intro.ipynb
@@ -50,9 +50,27 @@
     "- git\n",
     "- github\n",
     "- python\n",
+    "- python jupyter notebooks\n",
     "- github CI/CD\n",
     "\n",
-    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course."
+    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course. \n",
+    "\n",
+    "This course content template acts as a meta template; it provides you with instructions on how to use it while itself working and building like a course book would. We have included templates to be filled in where appropriate, and have included content for some of our courses to illustrate how it has been used. We hope that you find this helpful and enjoy the creating process."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "execution": {}
+   },
+   "source": [
+    "## Limitations\n",
+    "\n",
+    "It is highly encourage (borderline mandatory :p) that you stick to python packages that are easily installable using pip. If you need to install obscure supporting libraries, or specific verions of C compilers, this will cause you (and us) more headaches than necessary. If you want to use some obscure package, please try not to, or find another way to include the functionality of the desired package.\n",
+    "\n",
+    "It is also strongly advised that you decide on a pythong version for the book, stick to it, and make sure that all of your content creators are using the same version. Mixing python versions will also create a lot of headaches. What ever version you decide on, be sure to specify that in the github workflows. This template is using python 3.9.\n",
+    "\n",
+    "With love, the Neuromatch tech team"
    ]
   }
  ],

diff --git a/tutorials/W1D1_Instructions/W1D1_Tutorial2.ipynb b/tutorials/W1D1_Instructions/W1D1_Tutorial2.ipynb
@@ -177,8 +177,8 @@
     "\n",
     "In order for the workflows and scripts to work correctly, and for your book to properly build, you will need to **strictly** follow our folder heirarchy and naming conventions. This is what the scripts are expecting, and you will not be able to successfully build your course book if you deviate from the conventions. \n",
     "\n",
-    "- book/ (do not touch, this get automatically created/population in the publish workflow)\n",
-    "- projects/ (TODO: explain this in more depth)\n",
+    "- book/ (**do not touch**, this get automatically created/population in the publish workflow)\n",
+    "- projects/ (explained in tutorial 5)\n",
     "- tutorials/\n",
     "    - W#D#\\_DayName/ -> (ie. W1D1\\_InstructionsTemplate; This is strict! You must have the W#D#\\_ prefix followed by the name of the content for that day. The name **cannot** include special characters (i.e \\-, \\_) and must follow the format shown.\n",
     "        - static/\n",
@@ -194,7 +194,9 @@
     "See a working example below:\n",
     "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/folder-structure.png?raw=True' alt='folder structure image'/></p>\n",
     "\n",
-    "To reiterate, you do not need to worry about the student, instructor, or solutions directories. Those are automatically taken care of."
+    "To reiterate, you do not need to worry about the student, instructor, or solutions directories. Those are automatically taken care of.\n",
+    "\n",
+    "**NOTE**: W1D2 contains templates for tutorial creation. Where templates were not included, we provided examples from previous courses."
    ]
   },
   {
@@ -312,7 +314,6 @@
    },
    "source": [
     "## Section 5: Workflows\n",
-    "TODO: look into other workflows, ask spiros and ella\n",
     "\n",
     "There are two main workflows used to build the notebooks:\n",
     "- notebook-pr (automatically triggered when a PR is made onto the main repo)\n",
@@ -323,7 +324,17 @@
     "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/publish-book.gif?raw=True' alt='publish book gif'/></p>\n",
     "\n",
     "Point github pages to the gh-pages branch:\n",
-    "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/gh-pages.gif?raw=True' alt='github pages gif'/></p>\n"
+    "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/gh-pages.gif?raw=True' alt='github pages gif'/></p>\n",
+    "\n",
+    "Our course content is processed using github's compute machines. Then we generate the html versions of the course books and host them using github pages. Our scripts push the generated html to the gh-pages branch (do **not** touch this branch), which is why we need to point the pages setting to use the gh-pages branch.\n",
+    "\n",
+    "**NOTE**: Github supports adding custom urls for you hosted pages course book site. Contact our tech department lead Konstantine Tsafatinos and he will create the appropriate subdomain records for your new course. For example: **newcourse.neuromatch.io**. Custom domains are delicious, taste some of these:\n",
+    "\n",
+    "- [compneuro.neuromatch.io](https://compneuro.neuromatch.io)\n",
+    "- [deeplearning.neuromatch.io](https://deeplearning.neuromatch.io)\n",
+    "- [comptools.climatematch.io](https://comptools.climatematch.io)\n",
+    "\n",
+    "Enjoy! :)\n"
    ]
   },
   {
@@ -345,11 +356,6 @@
     "\n",
     "Happy content creating!"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
   }
  ],
  "metadata": {

diff --git a/tutorials/W1D1_Instructions/W1D1_Tutorial6.ipynb b/tutorials/W1D1_Instructions/W1D1_Tutorial6.ipynb
@@ -17,7 +17,7 @@
     "execution": {}
    },
    "source": [
-    "# Tutorial 6: Professional Developments\n",
+    "# Tutorial 6: Professional Development\n",
     "\n",
     "**Week 1, Day 1: Instructions**\n",
     "\n",

diff --git a/tutorials/W1D1_Instructions/instructor/W1D1_Intro.ipynb b/tutorials/W1D1_Instructions/instructor/W1D1_Intro.ipynb
@@ -50,9 +50,27 @@
     "- git\n",
     "- github\n",
     "- python\n",
+    "- python jupyter notebooks\n",
     "- github CI/CD\n",
     "\n",
-    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course."
+    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course. \n",
+    "\n",
+    "This course content template acts as a meta template; it provides you with instructions on how to use it while itself working and building like a course book would. We have included templates to be filled in where appropriate, and have included content for some of our courses to illustrate how it has been used. We hope that you find this helpful and enjoy the creating process."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "execution": {}
+   },
+   "source": [
+    "## Limitations\n",
+    "\n",
+    "It is highly encourage (borderline mandatory :p) that you stick to python packages that are easily installable using pip. If you need to install obscure supporting libraries, or specific verions of C compilers, this will cause you (and us) more headaches than necessary. If you want to use some obscure package, please try not to, or find another way to include the functionality of the desired package.\n",
+    "\n",
+    "It is also strongly advised that you decide on a pythong version for the book, stick to it, and make sure that all of your content creators are using the same version. Mixing python versions will also create a lot of headaches. What ever version you decide on, be sure to specify that in the github workflows. This template is using python 3.9.\n",
+    "\n",
+    "With love, the Neuromatch tech team"
    ]
   }
  ],

diff --git a/tutorials/W1D1_Instructions/instructor/W1D1_Tutorial2.ipynb b/tutorials/W1D1_Instructions/instructor/W1D1_Tutorial2.ipynb
@@ -42,7 +42,7 @@
    "source": [
     "___\n",
     "\n",
-    "# Tutorial Objectives\n",
+    "## Tutorial Objectives\n",
     "\n",
     "*Estimated timing of tutorial: [15 mins]*\n",
     "\n",
@@ -57,9 +57,7 @@
     "- learn how to update the *materials.yml* to reflect the newly created notebooks\n",
     "- learn the basic workflows\n",
     "\n",
-    "It is recommended that you read through all of this tutorial before starting to make changes, as all the topics are related to each other for a successful build of the notebooks.\n",
-    "\n",
-    "TODO: add projects info, prereqs info, and other sections info"
+    "It is recommended that you read through all of this tutorial before starting to make changes, as all the topics are related to each other for a successful build of the notebooks."
    ]
   },
   {
@@ -69,7 +67,7 @@
    },
    "source": [
     "---\n",
-    "# Setup\n",
+    "## Setup\n",
     "\n"
    ]
   },
@@ -96,7 +94,7 @@
    "source": [
     "---\n",
     "\n",
-    "# Section 1: How to enable github action\n",
+    "## Section 1: How to enable github action\n",
     " "
    ]
   },
@@ -131,7 +129,7 @@
    "source": [
     "---\n",
     "\n",
-    "# Section 2: How to create a PR\n",
+    "## Section 2: How to create a PR\n",
     "\n",
     "When creating content you want to add to the course book, you will need to have python and git installed. Afterwards, you will need to create a local python environment with all requirements for your code installed; including jyputer. Before starting to add content, you will need to create a new branch. Instructions [here](https://www.w3schools.com/git/git_branch.asp). \n",
     "\n",
@@ -153,7 +151,7 @@
     "execution": {}
    },
    "source": [
-    "## Section 2.1: Creating a PR\n",
+    "### Section 2.1: Creating a PR\n",
     "\n",
     "Once you have pushed the work on your new branch, you can create a PR onto the main branch. **NOTE**: This will trigger the processing workflow for the course content.\n",
     "\n",
@@ -175,12 +173,12 @@
     "execution": {}
    },
    "source": [
-    "# Section 3: Folder Structure and Naming Conventions\n",
+    "## Section 3: Folder Structure and Naming Conventions\n",
     "\n",
     "In order for the workflows and scripts to work correctly, and for your book to properly build, you will need to **strictly** follow our folder heirarchy and naming conventions. This is what the scripts are expecting, and you will not be able to successfully build your course book if you deviate from the conventions. \n",
     "\n",
-    "- book/ (do not touch, this get automatically created/population in the publish workflow)\n",
-    "- projects/ (TODO: explain this in more depth)\n",
+    "- book/ (**do not touch**, this get automatically created/population in the publish workflow)\n",
+    "- projects/ (explained in tutorial 5)\n",
     "- tutorials/\n",
     "    - W#D#\\_DayName/ -> (ie. W1D1\\_InstructionsTemplate; This is strict! You must have the W#D#\\_ prefix followed by the name of the content for that day. The name **cannot** include special characters (i.e \\-, \\_) and must follow the format shown.\n",
     "        - static/\n",
@@ -196,7 +194,9 @@
     "See a working example below:\n",
     "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/folder-structure.png?raw=True' alt='folder structure image'/></p>\n",
     "\n",
-    "To reiterate, you do not need to worry about the student, instructor, or solutions directories. Those are automatically taken care of."
+    "To reiterate, you do not need to worry about the student, instructor, or solutions directories. Those are automatically taken care of.\n",
+    "\n",
+    "**NOTE**: W1D2 contains templates for tutorial creation. Where templates were not included, we provided examples from previous courses."
    ]
   },
   {
@@ -205,7 +205,7 @@
     "execution": {}
    },
    "source": [
-    "## Section 3.1: Cell Tags (markings at the top of the cell)\n",
+    "### Section 3.1: Cell Tags (markings at the top of the cell)\n",
     "\n",
     "The workflows and processing scripts actively make use of predefined tags to determine how to process the cell. There are tags for video embeddeing, slide embedding, titles, exercises and solutions, etc. It is very important these instructions are followed **exactly**! Any deviations will break the pipeline. More details about the tags and how to use them can be found in W1D2_Tutorial1.ipynb of the template notebook.\n",
     "\n",
@@ -244,7 +244,7 @@
     "execution": {}
    },
    "source": [
-    "## Section 3.2: Add Images\n",
+    "### Section 3.2: Add Images\n",
     "\n",
     "Your images should live in the static directories. They can be grouped into the a static directory per day, or can be inside the general static directory for all tutorials. The important thing here is that you correctly link to the proper URL. You can directly add the following html into your markdown cells in order to add images.\n",
     "\n",
@@ -273,7 +273,7 @@
    "source": [
     "---\n",
     "\n",
-    "# Section 4: Add Content to the materials.yml File\n",
+    "## Section 4: Add Content to the materials.yml File\n",
     "\n",
     "The materials.yml file is used in our scripts to help verify links, populate the books, and create our table of contents. Be sure to **precisely** follow the structure outlined in the file. If you look at the materials.yml file for this template notebook, you will see the structure laid out in order for this book to properly build. There are comments in the file to further explain all the fields you will need to use. Here is an overview of the structure:\n",
     "\n",
@@ -313,8 +313,7 @@
     "execution": {}
    },
    "source": [
-    "# Section 5: Workflows\n",
-    "TODO: look into other workflows, ask spiros and ella\n",
+    "## Section 5: Workflows\n",
     "\n",
     "There are two main workflows used to build the notebooks:\n",
     "- notebook-pr (automatically triggered when a PR is made onto the main repo)\n",
@@ -325,7 +324,17 @@
     "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/publish-book.gif?raw=True' alt='publish book gif'/></p>\n",
     "\n",
     "Point github pages to the gh-pages branch:\n",
-    "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/gh-pages.gif?raw=True' alt='github pages gif'/></p>\n"
+    "<p align='center'><img src='https://github.com/neuromatch/course-content-template/blob/main/tutorials/static/gh-pages.gif?raw=True' alt='github pages gif'/></p>\n",
+    "\n",
+    "Our course content is processed using github's compute machines. Then we generate the html versions of the course books and host them using github pages. Our scripts push the generated html to the gh-pages branch (do **not** touch this branch), which is why we need to point the pages setting to use the gh-pages branch.\n",
+    "\n",
+    "**NOTE**: Github supports adding custom urls for you hosted pages course book site. Contact our tech department lead Konstantine Tsafatinos and he will create the appropriate subdomain records for your new course. For example: **newcourse.neuromatch.io**. Custom domains are delicious, taste some of these:\n",
+    "\n",
+    "- [compneuro.neuromatch.io](https://compneuro.neuromatch.io)\n",
+    "- [deeplearning.neuromatch.io](https://deeplearning.neuromatch.io)\n",
+    "- [comptools.climatematch.io](https://comptools.climatematch.io)\n",
+    "\n",
+    "Enjoy! :)\n"
    ]
   },
   {
@@ -335,7 +344,7 @@
    },
    "source": [
     "---\n",
-    "# Summary\n",
+    "## Summary\n",
     "\n",
     "Congrats! You now know:\n",
     "\n",

diff --git a/tutorials/W1D1_Instructions/instructor/W1D1_Tutorial6.ipynb b/tutorials/W1D1_Instructions/instructor/W1D1_Tutorial6.ipynb
@@ -17,7 +17,7 @@
     "execution": {}
    },
    "source": [
-    "# Tutorial 6: Professional Developments\n",
+    "# Tutorial 6: Professional Development\n",
     "\n",
     "**Week 1, Day 1: Instructions**\n",
     "\n",

diff --git a/tutorials/W1D1_Instructions/student/W1D1_Intro.ipynb b/tutorials/W1D1_Instructions/student/W1D1_Intro.ipynb
@@ -50,9 +50,27 @@
     "- git\n",
     "- github\n",
     "- python\n",
+    "- python jupyter notebooks\n",
     "- github CI/CD\n",
     "\n",
-    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course."
+    "Do not be discouraged if you are missing some of the prerequisites, we will give you a step by step explaination of how to go about building your course. \n",
+    "\n",
+    "This course content template acts as a meta template; it provides you with instructions on how to use it while itself working and building like a course book would. We have included templates to be filled in where appropriate, and have included content for some of our courses to illustrate how it has been used. We hope that you find this helpful and enjoy the creating process."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "execution": {}
+   },
+   "source": [
+    "## Limitations\n",
+    "\n",
+    "It is highly encourage (borderline mandatory :p) that you stick to python packages that are easily installable using pip. If you need to install obscure supporting libraries, or specific verions of C compilers, this will cause you (and us) more headaches than necessary. If you want to use some obscure package, please try not to, or find another way to include the functionality of the desired package.\n",
+    "\n",
+    "It is also strongly advised that you decide on a pythong version for the book, stick to it, and make sure that all of your content creators are using the same version. Mixing python versions will also create a lot of headaches. What ever version you decide on, be sure to specify that in the github workflows. This template is using python 3.9.\n",
+    "\n",
+    "With love, the Neuromatch tech team"
    ]
   }
  ],