From 7de6590929dde33f1e589433fd63768d7505fff0 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 15:44:14 -0400 Subject: [PATCH 01/19] duplicate sentence --- docs/Policies/hours_remote_vacation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/hours_remote_vacation.md b/docs/Policies/hours_remote_vacation.md index 33cd70f..c81286f 100644 --- a/docs/Policies/hours_remote_vacation.md +++ b/docs/Policies/hours_remote_vacation.md @@ -1,6 +1,6 @@ # Working hours, remote work, and vacation -As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. I'm generally in lab ~930-~6, and I try to be as available as possible during that time. As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. That being said, part of our job is being a contributing member to the lab community, and in my experience the spontaneous interactions we have here are some of the most impactful for the quality of our research. +As our work is predominantly theoretical/computational, we have a lot of flexibility around when and where we work. Please set your hours based on how you work best. That being said, part of our job is being a contributing member to the lab community, and in my experience the spontaneous interactions we have here are some of the most impactful for the quality of our research. I'm generally in lab ~930-~6, and I try to be as available as possible during that time. If it fits you, I would encourage you to plan one day a week where you work from home (or elsewhere out of office). This shift in perspective can be helpful for your work and I encourage you to take advantage of this time to think freely and critically about your project and current approaches. I do ask that you plan to attend lab meetings in person -- in my experience, remote attendance encourages people to listen (at best), rather than participate, in lab meetings. Also, I ask that you plan to be physically in lab 3-4 days a week. Of course, this can vary week to week and exceptions will be made to fit people’s circumstances. From 4ca12ee8fd2dc924339a6ce150713c0a2dc6e16e Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 16:08:09 -0400 Subject: [PATCH 02/19] merged travel.md into conferences_workshops.md and added some info on airports, still need to add some more details about public transit options --- docs/Policies/conferences_workshops.md | 10 ++++++++++ docs/Resources/travel.md | 3 --- 2 files changed, 10 insertions(+), 3 deletions(-) delete mode 100644 docs/Resources/travel.md diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index fc8600c..16b04cb 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -9,3 +9,13 @@ Please plan to **send me a draft of your abstract one week before deadline**. Th As with a paper submission, nothing goes out without all co-authors seeing and approving the final version. The exact number of conferences you should expect to present at per year will depend on your career stage, and status of your project. IMO the best times to present are when you're halfway through a project, and trying to figure out what the story is, and just after you've posted a preprint. + +To book travel and accommodation for conferences, use World Travel/Concur, Yale's platform for business travel. See [here](https://your.yale.edu/work-yale/campus-services/yale-travel-management) for more information. You can log into the Concur website [here](https://concur.yale.edu/). + +There is a training in Workday called ["Booking Federally Sponsored Travel with World Travel"](https://www.myworkday.com/yale/learning/course/1e7e093ab7a21001abc67bad56c90001?type=9882927d138b100019b928e75843018d&record=00f9b09f318e102c62781e428a3d0001) that you should complete in order to understand the restrictions on booking travel when using federal funds. + +You have a few options when it comes to airports: +- Bradley International Airport (BDL) in Hartford, CT +- Newark International Airport (EWR) in Newark, NJ +- John F. Kennedy Airport (JFK) in Queens, NYC +- LaGuardia Airport (LGA) in Queens, NYC diff --git a/docs/Resources/travel.md b/docs/Resources/travel.md deleted file mode 100644 index 75758a4..0000000 --- a/docs/Resources/travel.md +++ /dev/null @@ -1,3 +0,0 @@ -To book travel and accommodation for conferences, use World Travel/Concur, Yale's platform for business travel. See [here](https://your.yale.edu/work-yale/campus-services/yale-travel-management) for more information. You can log into the Concur website [here](https://concur.yale.edu/). - -There is a training in Workday called ["Booking Federally Sponsored Travel with World Travel"](https://www.myworkday.com/yale/learning/course/1e7e093ab7a21001abc67bad56c90001?type=9882927d138b100019b928e75843018d&record=00f9b09f318e102c62781e428a3d0001) that you should complete in order to understand the restrictions on booking travel when using federal funds. From c23045d135082d2808332eeb2131308cfdef0d00 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 19:27:55 -0400 Subject: [PATCH 03/19] added info on VS Code, linked a tutorial, and suggested a simple debugging script --- docs/Policies/code_software.md | 35 +++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/docs/Policies/code_software.md b/docs/Policies/code_software.md index 3c97461..d16905d 100644 --- a/docs/Policies/code_software.md +++ b/docs/Policies/code_software.md @@ -44,4 +44,37 @@ Patrick Mineault's code handbook above is a must-read before you start coding. I - Maintain good style. - This includes commenting, which should be done at the top of functions, classes, modules, files, etc. This helps both you and others understand code. - Pythonic code can be confusing sometimes; you'll need to make the tradeoff between clarity and brevity. - - Download a [linter](https://docs.astral.sh/ruff/) (e.g. Ruff) to help you format your code. \ No newline at end of file + - Download a [linter](https://docs.astral.sh/ruff/) (e.g. Ruff) to help you format your code. + +### VS Code +VS Code is a great IDE because it's open source (unlike e.g. PyCharm), highly customizable via extensions, and has great remote development support (which is important when working with the cluster). You can download it [here](https://code.visualstudio.com/Download). If you are unfamiliar with VS Code/IDEs in general, try a tutorial, such as [this one](https://code.visualstudio.com/docs/getstarted/getting-started). In particular, you should: +1. Link VS Code with your GitHub account +2. Open a repository, such as `Lab-Handbook` +3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) +4. Install the Python extension +5. Create an environment +6. Use the debugger. You can paste the script below into a `.py` file to try it out! + +``` +# debug_me.py +# A tiny script with an intentional bug to practice debugging in VS Code. + +# First, run the script normally to see the error. Then, set a breakpoint on the line +# with the division operation and run the debugger to inspect variables. + +def divide_numbers(a, b): + result = a / b + return result + +def main(): + numbers = [(10, 2), (5, 0), (8, 4)] + total = 0 + for x, y in numbers: + print(f"Dividing {x} by {y}") + total += divide_numbers(x, y) + + print("Average:", total / len(numbers)) + +if __name__ == "__main__": + main() +``` \ No newline at end of file From 288b2bae789a6035b614cc9622d8fec4b1538689 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 19:45:45 -0400 Subject: [PATCH 04/19] added info on travel to airport --- docs/Policies/conferences_workshops.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 16b04cb..5e289e3 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -15,7 +15,11 @@ To book travel and accommodation for conferences, use World Travel/Concur, Yale' There is a training in Workday called ["Booking Federally Sponsored Travel with World Travel"](https://www.myworkday.com/yale/learning/course/1e7e093ab7a21001abc67bad56c90001?type=9882927d138b100019b928e75843018d&record=00f9b09f318e102c62781e428a3d0001) that you should complete in order to understand the restrictions on booking travel when using federal funds. You have a few options when it comes to airports: -- Bradley International Airport (BDL) in Hartford, CT -- Newark International Airport (EWR) in Newark, NJ -- John F. Kennedy Airport (JFK) in Queens, NYC -- LaGuardia Airport (LGA) in Queens, NYC +- Bradley International Airport (BDL) in Hartford, CT: drive/Uber +- Newark International Airport (EWR) in Newark, NJ: direct Amtrak train from New Haven +- John F. Kennedy Airport (JFK) in Queens, NYC: Amtrak to LIRR or E train to AirTrain +- LaGuardia Airport (LGA) in Queens, NYC: Metro-North to Harlem-125th Street, then Uber or M60+ bus + +The three NYC airports are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). + +To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can tap your card or phone for the fare. \ No newline at end of file From 06acbffdfcca0ad96713c1cfb199153b28309f13 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 19:47:14 -0400 Subject: [PATCH 05/19] updated info on MTA --- docs/Policies/conferences_workshops.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 5e289e3..850ac27 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -22,4 +22,4 @@ You have a few options when it comes to airports: The three NYC airports are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). -To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can tap your card or phone for the fare. \ No newline at end of file +To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can use your card or phone for the fare on-site. \ No newline at end of file From 18718e9a90ce09e1349851231477c259ded4f7d1 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Mon, 27 Oct 2025 19:48:24 -0400 Subject: [PATCH 06/19] added info on EWR --- docs/Policies/conferences_workshops.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 850ac27..41292a4 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -20,6 +20,6 @@ You have a few options when it comes to airports: - John F. Kennedy Airport (JFK) in Queens, NYC: Amtrak to LIRR or E train to AirTrain - LaGuardia Airport (LGA) in Queens, NYC: Metro-North to Harlem-125th Street, then Uber or M60+ bus -The three NYC airports are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). +The three NYC airports (this includes Newark because of its proximity) are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can use your card or phone for the fare on-site. \ No newline at end of file From 3c76249bcda48f44c74dff5e668f26e59eff7924 Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 09:27:42 -0400 Subject: [PATCH 07/19] Update docs/Policies/conferences_workshops.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/Policies/conferences_workshops.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 41292a4..3438d38 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -20,6 +20,6 @@ You have a few options when it comes to airports: - John F. Kennedy Airport (JFK) in Queens, NYC: Amtrak to LIRR or E train to AirTrain - LaGuardia Airport (LGA) in Queens, NYC: Metro-North to Harlem-125th Street, then Uber or M60+ bus -The three NYC airports (this includes Newark because of its proximity) are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). +The three NYC airports (this includes Newark because of its proximity) are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](https://www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can use your card or phone for the fare on-site. \ No newline at end of file From 968c3d6307c76dc94ecc498eddb7e61c47102855 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Tue, 28 Oct 2025 11:26:25 -0400 Subject: [PATCH 08/19] moved travel info and vs_code tutorial to own readmes in resources, added debugging script --- .vscode/settings.json | 5 ++++ docs/Policies/code_software.md | 32 +------------------------- docs/Policies/conferences_workshops.md | 14 +---------- docs/Resources/debug_me.py | 21 +++++++++++++++++ docs/Resources/travel.md | 13 +++++++++++ docs/Resources/vs_code.md | 9 ++++++++ 6 files changed, 50 insertions(+), 44 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 docs/Resources/debug_me.py create mode 100644 docs/Resources/travel.md create mode 100644 docs/Resources/vs_code.md diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..a8c2003 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,5 @@ +{ + "python-envs.defaultEnvManager": "ms-python.python:conda", + "python-envs.defaultPackageManager": "ms-python.python:conda", + "python-envs.pythonProjects": [] +} \ No newline at end of file diff --git a/docs/Policies/code_software.md b/docs/Policies/code_software.md index d16905d..cef3018 100644 --- a/docs/Policies/code_software.md +++ b/docs/Policies/code_software.md @@ -47,34 +47,4 @@ Patrick Mineault's code handbook above is a must-read before you start coding. I - Download a [linter](https://docs.astral.sh/ruff/) (e.g. Ruff) to help you format your code. ### VS Code -VS Code is a great IDE because it's open source (unlike e.g. PyCharm), highly customizable via extensions, and has great remote development support (which is important when working with the cluster). You can download it [here](https://code.visualstudio.com/Download). If you are unfamiliar with VS Code/IDEs in general, try a tutorial, such as [this one](https://code.visualstudio.com/docs/getstarted/getting-started). In particular, you should: -1. Link VS Code with your GitHub account -2. Open a repository, such as `Lab-Handbook` -3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) -4. Install the Python extension -5. Create an environment -6. Use the debugger. You can paste the script below into a `.py` file to try it out! - -``` -# debug_me.py -# A tiny script with an intentional bug to practice debugging in VS Code. - -# First, run the script normally to see the error. Then, set a breakpoint on the line -# with the division operation and run the debugger to inspect variables. - -def divide_numbers(a, b): - result = a / b - return result - -def main(): - numbers = [(10, 2), (5, 0), (8, 4)] - total = 0 - for x, y in numbers: - print(f"Dividing {x} by {y}") - total += divide_numbers(x, y) - - print("Average:", total / len(numbers)) - -if __name__ == "__main__": - main() -``` \ No newline at end of file +VS Code is a great IDE because it's open source (unlike e.g. PyCharm), highly customizable via extensions, and has great remote development support (which is important when working with the cluster). You can download it [here](https://code.visualstudio.com/Download). If you are unfamiliar with VS Code/IDEs in general, see `Resources/vs_code.md` for more info on how to get started. \ No newline at end of file diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 3438d38..942485b 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -10,16 +10,4 @@ As with a paper submission, nothing goes out without all co-authors seeing and a The exact number of conferences you should expect to present at per year will depend on your career stage, and status of your project. IMO the best times to present are when you're halfway through a project, and trying to figure out what the story is, and just after you've posted a preprint. -To book travel and accommodation for conferences, use World Travel/Concur, Yale's platform for business travel. See [here](https://your.yale.edu/work-yale/campus-services/yale-travel-management) for more information. You can log into the Concur website [here](https://concur.yale.edu/). - -There is a training in Workday called ["Booking Federally Sponsored Travel with World Travel"](https://www.myworkday.com/yale/learning/course/1e7e093ab7a21001abc67bad56c90001?type=9882927d138b100019b928e75843018d&record=00f9b09f318e102c62781e428a3d0001) that you should complete in order to understand the restrictions on booking travel when using federal funds. - -You have a few options when it comes to airports: -- Bradley International Airport (BDL) in Hartford, CT: drive/Uber -- Newark International Airport (EWR) in Newark, NJ: direct Amtrak train from New Haven -- John F. Kennedy Airport (JFK) in Queens, NYC: Amtrak to LIRR or E train to AirTrain -- LaGuardia Airport (LGA) in Queens, NYC: Metro-North to Harlem-125th Street, then Uber or M60+ bus - -The three NYC airports (this includes Newark because of its proximity) are generally far cheaper and far better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets [here](https://www.amtrak.com) (you should buy them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to book in advance). - -To navigate the MTA (NYC's subway and bus system) you can use Google Maps or something like CityMapper for real-time arrival info. The MTA has tap-to-pay terminals so you can use your card or phone for the fare on-site. \ No newline at end of file +See `Resources/travel.md` for information on booking travel. \ No newline at end of file diff --git a/docs/Resources/debug_me.py b/docs/Resources/debug_me.py new file mode 100644 index 0000000..8a09db7 --- /dev/null +++ b/docs/Resources/debug_me.py @@ -0,0 +1,21 @@ +# debug_me.py +# A tiny script with an intentional bug to practice debugging in VS Code. + +# First, run the script normally to see the error. Then, set a breakpoint on the line +# with the division operation and run the debugger to inspect variables. + +def divide_numbers(a, b): + result = a / b + return result + +def main(): + numbers = [(10, 2), (5, 0), (8, 4)] + total = 0 + for x, y in numbers: + print(f"Dividing {x} by {y}") + total += divide_numbers(x, y) + + print("Average:", total / len(numbers)) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/docs/Resources/travel.md b/docs/Resources/travel.md new file mode 100644 index 0000000..bb9fd36 --- /dev/null +++ b/docs/Resources/travel.md @@ -0,0 +1,13 @@ +To book travel and accommodation for conferences, use World Travel/Concur, Yale's platform for business travel. See [here](https://your.yale.edu/work-yale/campus-services/yale-travel-management) for more information. You can log into the Concur website [here](https://concur.yale.edu/). + +There is a training in Workday called ["Booking Federally Sponsored Travel with World Travel"](https://www.myworkday.com/yale/learning/course/1e7e093ab7a21001abc67bad56c90001?type=9882927d138b100019b928e75843018d&record=00f9b09f318e102c62781e428a3d0001) that you should complete in order to understand the restrictions on booking travel when using federal funds. + +You have a few options when it comes to airports: +- Bradley International Airport (BDL) in Hartford, CT: drive/Uber +- Newark International Airport (EWR) in Newark, NJ: direct Amtrak train from New Haven +- John F. Kennedy Airport (JFK) in Queens, NYC: Amtrak to LIRR or E train to AirTrain +- LaGuardia Airport (LGA) in Queens, NYC: Metro-North to Harlem-125th Street, then Uber or M60+ bus + +The three NYC airports (including EWR) are generally far cheaper and better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets in [Concur](https://concur.yale.edu/) (you should book them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to buy in advance). + +To navigate the MTA (NYC's public transit system) use Google Maps or e.g. CityMapper for real-time arrival info. The MTA has tap-to-pay terminals, so you can purchase ticket on-site using your card or phone. \ No newline at end of file diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md new file mode 100644 index 0000000..27ab6df --- /dev/null +++ b/docs/Resources/vs_code.md @@ -0,0 +1,9 @@ +To get started with VS try a tutorial, such as [this one](https://code.visualstudio.com/docs/getstarted/getting-started). The program itself will also give you some tips. + +Some basic tips to get started: +1. Link VS Code with your GitHub account +2. Open a repository, such as `Lab-Handbook` +3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) +4. Install the Python extension +5. Create an environment +6. Use the debugger. You can run `Resources/debug_me.py` to try it out! \ No newline at end of file From 7c184d16e2f18f9c9e53bb5f1a7199de33ab8e72 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Tue, 28 Oct 2025 11:42:02 -0400 Subject: [PATCH 09/19] added info on debugging script and lab repo, updated .yml file --- docs/Resources/vs_code.md | 2 +- mkdocs.yml | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md index 27ab6df..0d8a5b3 100644 --- a/docs/Resources/vs_code.md +++ b/docs/Resources/vs_code.md @@ -6,4 +6,4 @@ Some basic tips to get started: 3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) 4. Install the Python extension 5. Create an environment -6. Use the debugger. You can run `Resources/debug_me.py` to try it out! \ No newline at end of file +6. Use the debugger. You can copy `Resources/debug_me.py` to a new repo to try it out! You can create a lab repo that you will also use for the pRNN tutorial. Just make sure that you don't try to push it to this repo. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 39576ee..f26ee0e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,6 +12,7 @@ nav: - Adobe: Resources/adobe.md - Basic Github: Resources/basic_github.md - Booking Rooms: Resources/booking.md + - Debugging script: Resources/debug_me.md - GenAI: Resources/gen_ai.md - HPC: Resources/hpc.md - Mailing Lists: Resources/mailing_lists.md @@ -22,5 +23,6 @@ nav: - Doing Science: Resources/science_general.md - Travel: Resources/travel.md - VPN: Resources/vpn.md + - VS Code: Resources/vs_code.md - Onboarding: onboarding.md - Contact: contact.md From 19403006ade8beea3d3968f80196fb6e05722b32 Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 11:51:53 -0400 Subject: [PATCH 10/19] Update instructions for using the debugger --- docs/Resources/vs_code.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md index 0d8a5b3..80bb2d1 100644 --- a/docs/Resources/vs_code.md +++ b/docs/Resources/vs_code.md @@ -6,4 +6,4 @@ Some basic tips to get started: 3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) 4. Install the Python extension 5. Create an environment -6. Use the debugger. You can copy `Resources/debug_me.py` to a new repo to try it out! You can create a lab repo that you will also use for the pRNN tutorial. Just make sure that you don't try to push it to this repo. \ No newline at end of file +6. Use the debugger. You can copy `Resources/debug_me.py` to try it out! If you want, you can create a new project repo that you will also use for the pytorch tutorial as part of your first project. From 922155aa723075c9b0156a3843c4f99f16cb9492 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Tue, 28 Oct 2025 13:08:24 -0400 Subject: [PATCH 11/19] deleted vscode dir --- .vscode/settings.json | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index a8c2003..0000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "python-envs.defaultEnvManager": "ms-python.python:conda", - "python-envs.defaultPackageManager": "ms-python.python:conda", - "python-envs.pythonProjects": [] -} \ No newline at end of file From b369ade36c0dd55efc1384420abe5fab66d641c8 Mon Sep 17 00:00:00 2001 From: Andrea Cumpelik Date: Tue, 28 Oct 2025 13:10:35 -0400 Subject: [PATCH 12/19] updated link to debugging script in vs_code.md --- docs/Resources/vs_code.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md index 80bb2d1..8e34372 100644 --- a/docs/Resources/vs_code.md +++ b/docs/Resources/vs_code.md @@ -6,4 +6,4 @@ Some basic tips to get started: 3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) 4. Install the Python extension 5. Create an environment -6. Use the debugger. You can copy `Resources/debug_me.py` to try it out! If you want, you can create a new project repo that you will also use for the pytorch tutorial as part of your first project. +6. Use the debugger. You can copy `https://levensteinlab.github.io/Lab-Handbook/Resources/debug_me.py` to try it out! If you want, you can create a new project repo that you will also use for the pytorch tutorial as part of your first project. \ No newline at end of file From 318f537aa6c3b3919ce6aac1c2afe47468cca5a3 Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:37:33 -0400 Subject: [PATCH 13/19] Improve VS Code section with updated tutorial link Updated the reference for the VS Code tutorial link for better guidance. --- docs/Policies/code_software.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/code_software.md b/docs/Policies/code_software.md index cef3018..703e3f0 100644 --- a/docs/Policies/code_software.md +++ b/docs/Policies/code_software.md @@ -47,4 +47,4 @@ Patrick Mineault's code handbook above is a must-read before you start coding. I - Download a [linter](https://docs.astral.sh/ruff/) (e.g. Ruff) to help you format your code. ### VS Code -VS Code is a great IDE because it's open source (unlike e.g. PyCharm), highly customizable via extensions, and has great remote development support (which is important when working with the cluster). You can download it [here](https://code.visualstudio.com/Download). If you are unfamiliar with VS Code/IDEs in general, see `Resources/vs_code.md` for more info on how to get started. \ No newline at end of file +VS Code is a great IDE because it's open source (unlike e.g. PyCharm), highly customizable via extensions, and has great remote development support (which is important when working with the cluster). You can download it [here](https://code.visualstudio.com/Download). If you are unfamiliar with VS Code/IDEs in general, see the [VS Code tutorial](https://levensteinlab.github.io/Lab-Handbook/Resources/vs_code) for more info on how to get started. From f5a86f9b6d58b79ec3d0c97b73998715652e532d Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:38:30 -0400 Subject: [PATCH 14/19] Update travel resource link in workshop policy --- docs/Policies/conferences_workshops.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 942485b..6015ce0 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -10,4 +10,4 @@ As with a paper submission, nothing goes out without all co-authors seeing and a The exact number of conferences you should expect to present at per year will depend on your career stage, and status of your project. IMO the best times to present are when you're halfway through a project, and trying to figure out what the story is, and just after you've posted a preprint. -See `Resources/travel.md` for information on booking travel. \ No newline at end of file +See [Resouces - Travel](https://levensteinlab.github.io/Lab-Handbook/Resources/travel/) for information on booking travel. From 6a9e93dca4a1eb27e2a43f01392529e794c5561e Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:39:58 -0400 Subject: [PATCH 15/19] Update debugger resource link in vs_code.md --- docs/Resources/vs_code.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md index 8e34372..80bb2d1 100644 --- a/docs/Resources/vs_code.md +++ b/docs/Resources/vs_code.md @@ -6,4 +6,4 @@ Some basic tips to get started: 3. Try out the terminal (e.g. try `echo $SHELL` to see which shell your computer runs by default) 4. Install the Python extension 5. Create an environment -6. Use the debugger. You can copy `https://levensteinlab.github.io/Lab-Handbook/Resources/debug_me.py` to try it out! If you want, you can create a new project repo that you will also use for the pytorch tutorial as part of your first project. \ No newline at end of file +6. Use the debugger. You can copy `Resources/debug_me.py` to try it out! If you want, you can create a new project repo that you will also use for the pytorch tutorial as part of your first project. From 70f24e5f8125ef61c7a31d55f07e2807eecef80c Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:44:05 -0400 Subject: [PATCH 16/19] Update mkdocs.yml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- mkdocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index f26ee0e..e28e45c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,7 +12,6 @@ nav: - Adobe: Resources/adobe.md - Basic Github: Resources/basic_github.md - Booking Rooms: Resources/booking.md - - Debugging script: Resources/debug_me.md - GenAI: Resources/gen_ai.md - HPC: Resources/hpc.md - Mailing Lists: Resources/mailing_lists.md From e30eb9b3ac81ea7e6d4cabb6f35c4aa638bc76c6 Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:44:25 -0400 Subject: [PATCH 17/19] Update docs/Policies/conferences_workshops.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/Policies/conferences_workshops.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Policies/conferences_workshops.md b/docs/Policies/conferences_workshops.md index 6015ce0..bc1bf94 100644 --- a/docs/Policies/conferences_workshops.md +++ b/docs/Policies/conferences_workshops.md @@ -10,4 +10,4 @@ As with a paper submission, nothing goes out without all co-authors seeing and a The exact number of conferences you should expect to present at per year will depend on your career stage, and status of your project. IMO the best times to present are when you're halfway through a project, and trying to figure out what the story is, and just after you've posted a preprint. -See [Resouces - Travel](https://levensteinlab.github.io/Lab-Handbook/Resources/travel/) for information on booking travel. +See [Resources - Travel](https://levensteinlab.github.io/Lab-Handbook/Resources/travel/) for information on booking travel. From c3505a95a4575a2ec3a53d4d5a2c9cf5473a1edb Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:44:37 -0400 Subject: [PATCH 18/19] Update docs/Resources/vs_code.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/Resources/vs_code.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Resources/vs_code.md b/docs/Resources/vs_code.md index 80bb2d1..925e6e5 100644 --- a/docs/Resources/vs_code.md +++ b/docs/Resources/vs_code.md @@ -1,4 +1,4 @@ -To get started with VS try a tutorial, such as [this one](https://code.visualstudio.com/docs/getstarted/getting-started). The program itself will also give you some tips. +To get started with VS Code try a tutorial, such as [this one](https://code.visualstudio.com/docs/getstarted/getting-started). The program itself will also give you some tips. Some basic tips to get started: 1. Link VS Code with your GitHub account From 0d2191a4795922b0d1a00e598794525cc755001f Mon Sep 17 00:00:00 2001 From: Dan Levenstein Date: Tue, 28 Oct 2025 13:44:48 -0400 Subject: [PATCH 19/19] Update docs/Resources/travel.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/Resources/travel.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Resources/travel.md b/docs/Resources/travel.md index bb9fd36..4b34cef 100644 --- a/docs/Resources/travel.md +++ b/docs/Resources/travel.md @@ -10,4 +10,4 @@ You have a few options when it comes to airports: The three NYC airports (including EWR) are generally far cheaper and better connected. The direct Amtrak train from New Haven to Newark/EWR makes that the most convenient option. You can book Amtrak tickets in [Concur](https://concur.yale.edu/) (you should book them in advance) or use the [TrainTime App](https://www.mta.info/traintime) to buy Metro-North/LIRR tickets (less important to buy in advance). -To navigate the MTA (NYC's public transit system) use Google Maps or e.g. CityMapper for real-time arrival info. The MTA has tap-to-pay terminals, so you can purchase ticket on-site using your card or phone. \ No newline at end of file +To navigate the MTA (NYC's public transit system) use Google Maps or e.g. CityMapper for real-time arrival info. The MTA has tap-to-pay terminals, so you can purchase a ticket on-site using your card or phone. \ No newline at end of file