From e7b4622244e65bbe8b1db34fc44dcd3cf0a0c26a Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 07:35:23 +0000 Subject: [PATCH 1/9] Add conda environment file --- environment.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..2d834b3 --- /dev/null +++ b/environment.yml @@ -0,0 +1,22 @@ +name: nest-simulator-binder-environment +channels: + - conda-forge +dependencies: + - python >= 3.10 + - pip + - nest + +- pip: + + # To build and work with PyNEST + - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt + + # To run NEST testsuite + - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt + + # To build NEST documentation + - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_docs.txt + + # To run NEST Server + - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt + \ No newline at end of file From ef79c3867e21a7c0ab5e888d18d00020996d342f Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 07:44:20 +0000 Subject: [PATCH 2/9] Fix sorting --- environment.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 2d834b3..71302d3 100644 --- a/environment.yml +++ b/environment.yml @@ -5,18 +5,13 @@ dependencies: - python >= 3.10 - pip - nest - -- pip: - + - pip: # To build and work with PyNEST - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt - # To run NEST testsuite - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt - # To build NEST documentation - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_docs.txt - # To run NEST Server - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt \ No newline at end of file From c8ec962c412ed159dac23dda57ee6f9054c6c308 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 07:45:50 +0000 Subject: [PATCH 3/9] Fix naming --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 71302d3..f49ea47 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: dependencies: - python >= 3.10 - pip - - nest + - nest-simulator - pip: # To build and work with PyNEST - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt From ef11f3bda264cb24af34c42a2383ef4eaeb181f1 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 07:52:48 +0000 Subject: [PATCH 4/9] Disable install buildtools, issue building mpi4py --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index f49ea47..6fd9e67 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ dependencies: - nest-simulator - pip: # To build and work with PyNEST - - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt + # - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt # To run NEST testsuite - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt # To build NEST documentation From 7dbbf1340aa33db3720a3532e231c4e0d692e989 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 08:14:20 +0000 Subject: [PATCH 5/9] Try with no pip dependencies --- environment.yml | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/environment.yml b/environment.yml index 6fd9e67..b4e6e2c 100644 --- a/environment.yml +++ b/environment.yml @@ -1,17 +1,11 @@ name: nest-simulator-binder-environment channels: - conda-forge + - defaults dependencies: - - python >= 3.10 - - pip + - matplotlib - nest-simulator - - pip: - # To build and work with PyNEST - # - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_pynest.txt - # To run NEST testsuite - - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt - # To build NEST documentation - - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_docs.txt - # To run NEST Server - - -r https://raw.githubusercontent.com/nest/nest-simulator/master/requirements_testing.txt - \ No newline at end of file + - numpy + - pandas + - pip + - python >= 3.10 \ No newline at end of file From 11ff33c726875d6247701b73ad7c286a258bf3cd Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 8 May 2024 08:15:05 +0000 Subject: [PATCH 6/9] Add defaults channel --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index b4e6e2c..72b73c6 100644 --- a/environment.yml +++ b/environment.yml @@ -1,7 +1,7 @@ name: nest-simulator-binder-environment channels: - conda-forge - - defaults + - defaults dependencies: - matplotlib - nest-simulator From 757d8353493bcf4415bb7b3af034d9d27030a916 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Tue, 14 May 2024 08:58:46 +0000 Subject: [PATCH 7/9] Add elephant and PyNN via pip --- environment.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 72b73c6..8175985 100644 --- a/environment.yml +++ b/environment.yml @@ -7,5 +7,9 @@ dependencies: - nest-simulator - numpy - pandas - - pip - - python >= 3.10 \ No newline at end of file + - python >= 3.10 + - pip: + - elephant + - viziphant + - neo + - PyNN \ No newline at end of file From 50cabf37a4acd50e34a7e8d07ff4cd8bc727eae5 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Tue, 14 May 2024 11:35:29 +0000 Subject: [PATCH 8/9] fix pip in the dependencies --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 8175985..bec2093 100644 --- a/environment.yml +++ b/environment.yml @@ -7,6 +7,7 @@ dependencies: - nest-simulator - numpy - pandas + - pip - python >= 3.10 - pip: - elephant From 41570938a31536851c5bd2f6887d6ada26070c43 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Thu, 6 Jun 2024 10:13:52 +0000 Subject: [PATCH 9/9] Add nestml to binder environment --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index bec2093..0ffaa1a 100644 --- a/environment.yml +++ b/environment.yml @@ -5,6 +5,7 @@ channels: dependencies: - matplotlib - nest-simulator + - nestml - numpy - pandas - pip