-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
baec063
commit 7e6b6b2
Showing
8 changed files
with
81 additions
and
57 deletions.
There are no files selected for viewing
File renamed without changes.
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,23 +1,29 @@ | ||
# Local set-up using pip and venv | ||
|
||
1) Ensure that you have python 3.9 and pip installed on your computer: | ||
1. Ensure that python >=3.9 and pip are installed (if not, install python >=3.9) | ||
``` | ||
python -V # should return >=3.9 | ||
python -V # should return >=3.9 | ||
python -m pip -V | ||
``` | ||
|
||
2) Install virtualenv: `python -m pip install virtualenv` | ||
2. Install virtualenv: `python -m pip install virtualenv` | ||
|
||
3) Create virtual environment: `python -m venv aeon` | ||
3. Create virtual environment: `python -m venv aeon` | ||
|
||
4) Activate the virtual environment and install the code dependencies: | ||
4. Activate the virtual environment and install the code dependencies: | ||
``` | ||
source aeon/bin/activate | ||
python -m pip install -r requirements.txt | ||
python -m pip install -e . | ||
``` | ||
|
||
5) Using the virtual environment: | ||
5. Optionally install the development dependencies: | ||
``` | ||
source aeon/bin/activate | ||
python -m pip install -e .[dev] | ||
``` | ||
|
||
6. Using the virtual environment: | ||
|
||
`source aeon/bin/activate` activates the virtual environment. | ||
`source aeon/bin/activate` activates the virtual environment; any commands now run within this terminal will take place within the virtual environment. | ||
|
||
`deactivate` deactivates the virtual environment. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,20 +1,27 @@ | ||
# Remote set-up using miniconda and conda | ||
|
||
1) Add miniconda to your system path and create the `aeon` python env from the `env.yml` file: | ||
1. Add miniconda to your system path and create the `aeon` python env from the `env.yml` file: | ||
|
||
``` | ||
module load miniconda | ||
conda env create -f env.yml | ||
conda env create -f env_config/env.yml | ||
``` | ||
|
||
2) Using the virtual environment: | ||
2. Optionally install development dependencies: | ||
|
||
`conda activate aeon`: activates the virtual environment; any commands now run within this terminal will take place within the virtual environment. | ||
``` | ||
conda activate aeon | ||
conda env update -f env_config/env_dev.yml | ||
``` | ||
|
||
3. Using the virtual environment: | ||
|
||
`conda deactivate aeon`: deactivates the virtual environment. | ||
- `conda activate aeon`: activates the virtual environment; any commands now run within this terminal will take place within the virtual environment. | ||
|
||
3) (Optional) Add commands to `.profile` to add miniconda as an environment module and Bonsai and its dependencies to your system path on startup: | ||
- `conda deactivate aeon`: deactivates the virtual environment. | ||
|
||
Copy the commands in the `.profile` file in this folder to your HPC home directory `.profile` file. | ||
4. (Optional) Add commands to the `.profile` file to add miniconda as an environment module and Bonsai and its dependencies to your system path on startup (this will be initialized each time you SSH into the HPC). | ||
|
||
- Copy the commands in the `.profile` file in this folder to your HPC home directory `.profile` file. | ||
|
||
4) For instructions on developing within the `aeon` environment, see [`developing_on_hpc.md`](./developing_on_hpc.md) | ||
5. For instructions on developing within the `aeon` environment, see [`developing_on_hpc.md`](./developing_on_hpc.md) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,25 +1,31 @@ | ||
# Remote set-up using pip and venv | ||
|
||
1) Ensure that you have python 3.9 and pip installed on your computer: | ||
1. Ensure that python >=3.9 and pip are installed (if not, install python >=3.9) | ||
``` | ||
python -V # should return >=3.9 | ||
python -V # should return >=3.9 | ||
python -m pip -V | ||
``` | ||
|
||
2) Install virtualenv: `python -m pip install virtualenv` | ||
2. Install virtualenv: `python -m pip install virtualenv` | ||
|
||
3) Create virtual environment: `python -m venv aeon` | ||
3. Create virtual environment: `python -m venv aeon` | ||
|
||
4) Activate the virtual environment and install the code dependencies: | ||
4. Activate the virtual environment and install the code dependencies: | ||
``` | ||
source aeon/bin/activate | ||
python -m pip install -r requirements.txt | ||
python -m pip install -e . | ||
``` | ||
|
||
5) Using the virtual environment: | ||
5. Optionally install the development dependencies: | ||
``` | ||
source aeon/bin/activate | ||
python -m pip install -e .[dev] | ||
``` | ||
|
||
6. Using the virtual environment: | ||
|
||
`source aeon/bin/activate` activates the virtual environment. | ||
`source aeon/bin/activate` activates the virtual environment; any commands now run within this terminal will take place within the virtual environment. | ||
|
||
`deactivate` deactivates the virtual environment. | ||
|
||
6) For instructions on developing within the `aeon` environment, see [`developing_on_hpc.md`](./developing_on_hpc.md) | ||
7. For instructions on developing within the `aeon` environment, see [`developing_on_hpc.md`](./developing_on_hpc.md) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters