basic Python-Julia communication

.github/workflows/CompatHelper.yml

-name: CompatHelper
-on:
-  schedule:
-    - cron: 0 0 * * *
-  workflow_dispatch:
-jobs:
-  CompatHelper:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

-name: TagBot
-on:
-  issue_comment:
-    types:
-      - created
-  workflow_dispatch:
-jobs:
-  TagBot:
-    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
-    runs-on: ubuntu-latest
-    steps:
-      - uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitlab-ci.yml

@@ -16,11 +16,10 @@
         c, t = get_summary(process_folder())
         using Printf
         @printf "Test coverage %.2f%%\n" 100c / t'
-Julia 1.0:
-  image: julia:1.0
+Julia 1.6:
+  image: julia:1.6
   extends:
     - .script
-    - .coverage
 Julia 1.7:
   image: julia:1.7
   extends:

Artifacts.toml

+[chore_sample_output]
+git-tree-sha1 = "21f352668bf80009c68c3487fb464df477dc2b7a"
+lazy = true
+
+	[[chore_sample_output.download]]
+	url = "https://gitlab.pasteur.fr/nyx/artefacts/-/raw/master/PlanarLarvae/chore_sample_output.tar.gz?inline=false"
+	sha256 = "56845fa23cf53a58df33f6a4daf48e0a031f3c7e920f9badd62ae07f350b62d8"
+
+[sample_trxmat_file]
+git-tree-sha1 = "e131dc0168d075ba884f26435f626cdfd6b13365"
+lazy = true
+
+	[[sample_trxmat_file.download]]
+	url = "http://dl.pasteur.fr/fop/wGF4Ypgs/trx.mat.tgz"
+	sha256 = "4cf2656c7917c623d668382c93d21ce3ef7da67255ee0efd596f7e0b40a84947"

Project.toml

@@ -3,8 +3,12 @@ uuid = "e551f703-3b82-4335-b341-d497b48d519b"
 authors = ["François Laurent", "Institut Pasteur"]
 version = "0.1.0"
 
+[deps]
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+
 [compat]
-julia = "1"
+julia = "1.6"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

pyproject.toml

+[tool.poetry]
+name = "TaggingBackends"
+version = "0.1.0"
+description = ""
+authors = ["François Laurent <francois.laurent@pasteur.fr>"]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+julia = "^0.5.7"
+
+[tool.poetry.dev-dependencies]
+pytest = "^5.2"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

taggingbackends/__init__.py

+__version__ = '0.1.0'

test/makedata.jl

+using LazyArtifacts
+
+function make_test_data(target="chore_sample_outline")
+    # we want `targets` to be mutable
+    isstr = target isa String
+    if isstr
+        targets = [target]
+    else
+        # copy
+        targets = Vector{String}(target)
+    end
+    for t in 1:length(targets)
+        target = targets[t]
+        dir = nothing
+        # call the `artifact` string macro
+        if startswith(target, "chore_sample_")
+            artefact = artifact"chore_sample_output"
+            dir = "chore_sample_output"
+            filetype = target[length("chore_sample_")+1:end]
+            if filetype ∉ ("outline", "spine")
+                throw(DomainError("unknown Chore output: " * filetype))
+            end
+            filename = "20150701_105504@FCF_attP2_1500062@UAS_Chrimson_Venus_X_0070@t15@r_LED50_30s2x15s30s#n#n#n@100." * filetype
+        elseif target == "sample_trxmat_file"
+            artefact = artifact"sample_trxmat_file"
+            filename = "trx.mat"
+        else
+            throw(DomainError("unknown artefact: " * target))
+        end
+        # return path to individual file instead
+        if isnothing(dir)
+            path = joinpath(artefact, filename)
+        else
+            path = joinpath(artefact, dir, filename)
+        end
+        targets[t] = path
+    end
+    if isstr
+        targets = targets[1]
+    end
+    return targets
+end

test/makedata.py

+from pathlib import Path
+project_dir = Path(__file__).parent.parent
+
+import os
+os.environ['JULIA_PROJECT'] = str(project_dir)
+
+from julia import Julia
+Julia(compiled_modules=False)
+
+from julia import Main
+Main.include("test/makedata.jl")
+
+def make_test_data(target="sample_trxmat_file"):
+    return Main.make_test_data(f"{target}")
+
+import pytest
+
+@pytest.fixture
+def sample_trxmat_file():
+    return make_test_data("sample_trxmat_file")
+

test/test_taggingbackends.py

+from taggingbackends import __version__
+
+
+def test_version():
+    assert __version__ == '0.1.0'
+
+
+import os.path
+from .makedata import sample_trxmat_file
+
+class TestDataFiles:
+    """
+    Test reading data from files.
+    """
+    def test_get_trxmat_file(self, sample_trxmat_file):
+        print(sample_trxmat_file)
+        assert os.path.isfile(sample_trxmat_file)
+