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Merged
MariaHei merged 15 commits into from
Jan 24, 2026
Merged

Remove conda and add python package installation to CI #133

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a2b096a
Remove conda and add python package installation to CI
MariaHei Jan 21, 2026
3e6c97c
Improve CI python setup
MariaHei Jan 21, 2026
49cb1b4
change when CI is run
MariaHei Jan 21, 2026
81aec87
build pycall later
MariaHei Jan 21, 2026
ac2f8b2
resolve manifest before building pycall
MariaHei Jan 21, 2026
4c812d8
roll back
MariaHei Jan 21, 2026
0cbb4b7
run pyndl tests on windows as well
MariaHei Jan 21, 2026
d0817ea
don't restrict upper version of julia
MariaHei Jan 21, 2026
e6e7aa3
Set python to python set up in CI
MariaHei Jan 21, 2026
775c16f
explicitly set python env
MariaHei Jan 21, 2026
6afcfdc
remove pycall cache
MariaHei Jan 21, 2026
e072f0e
try again
MariaHei Jan 21, 2026
07f2c22
Don't run pyndl tests on mac
MariaHei Jan 21, 2026
172df61
check for apple
MariaHei Jan 21, 2026
d7e5056
run on all julia versions
MariaHei Jan 21, 2026
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23 changes: 13 additions & 10 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: CI
on:
- push
- pull_request
- workflow_dispatch
push:
branches:
- main
tags: '*'
pull_request:
workflow_dispatch:
jobs:
test:
name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
Expand All @@ -21,7 +24,6 @@ jobs:
- macOS-latest
- windows-latest
python-version:
- 3.8
- 3.12
arch:
- x64
Expand All @@ -43,15 +45,14 @@ jobs:
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
id: setup-python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install pyndl (Linux)
if: ${{ runner.os == 'Linux' }}
- name: Install Python dependencies
run: |
pip install pyndl
env:
PYTHON: 3.8
python -m pip install --upgrade pip
pip install netcdf4 cython pandas xarray numpy pyndl
- uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.version }}
Expand All @@ -68,8 +69,10 @@ jobs:
${{ runner.os }}-
- uses: julia-actions/julia-buildpkg@latest
env:
PYTHON: python
PYTHON: ${{ steps.setup-python.outputs.python-path }}
- uses: julia-actions/julia-runtest@latest
env:
PYTHON: ${{ steps.setup-python.outputs.python-path }}
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v1
with:
Expand Down
4 changes: 1 addition & 3 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@ authors = ["Xuefeng Luo", "Maria Heitmeier"]
BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataLoaders = "2e981812-ef13-4a9c-bfa0-ab13047b12a9"
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
Expand All @@ -29,7 +28,6 @@ SuiteSparse = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
BSON = "0.3"
BenchmarkTools = "1.0 - 1.5"
CSV = "0.10"
Conda = "1.10.3"
DataFrames = "0.21, 1.6"
DataLoaders = "0.1.3"
DataStructures = "0.18"
Expand All @@ -41,7 +39,7 @@ GZip = "0.6.2"
ProgressMeter = "1.9"
Requires = "1.3"
Statistics = "1.3 - 1.11.1"
julia = "1.9 - 1.12"
julia = "1.9"

[extras]
SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
Expand Down
1 change: 0 additions & 1 deletion test/Project.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataLoaders = "2e981812-ef13-4a9c-bfa0-ab13047b12a9"
Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
Expand Down
13 changes: 0 additions & 13 deletions test/pyndl_tests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,19 +3,6 @@ using PyCall
using JudiLing
using CSV, DataFrames

using Conda

@info "Installing pyndl dependencies..."
Conda.add("numpy", Conda.ROOTENV)
Conda.add("cython", Conda.ROOTENV)
Conda.add("pandas", Conda.ROOTENV)
Conda.add("xarray", Conda.ROOTENV)
Conda.add("netcdf4", Conda.ROOTENV)

@info "Installing pyndl..."
pip_exe = joinpath(Conda.PYTHONDIR, "pip")
run(`$pip_exe install pyndl`)


train = DataFrame(CSV.File(joinpath("data", "careful", "latin_train.csv")))
val = DataFrame(CSV.File(joinpath("data", "careful", "latin_val.csv")))
Expand Down
2 changes: 1 addition & 1 deletion test/runtests.jl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
using SafeTestsets

if !Sys.iswindows()
if !Sys.isapple()
@safetestset "pyndl tests" begin
include("pyndl_tests.jl")
end
Expand Down
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