Merge remote-tracking branch 'origin/main' into v1

Author: Christopher Doris

.JuliaFormatter.toml

@@ -0,0 +1,8 @@
+ignore = [
+    "examples",
+    ".git",
+    ".CondaPkg",
+    ".ipynb_checkpoints",
+    ".pytest_cache",
+    ".venv",
+]

.github/workflows/tagbot.yml

@@ -4,6 +4,22 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -12,4 +28,6 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
           ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

.github/workflows/tests-nightly.yml

@@ -38,6 +38,7 @@ jobs:
       - uses: julia-actions/julia-runtest@v1
         env:
           JULIA_DEBUG: PythonCall
+          JULIA_NUM_THREADS: '2'
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:

.github/workflows/tests.yml

@@ -45,6 +45,7 @@ jobs:
         uses: julia-actions/julia-runtest@v1
         env:
           JULIA_DEBUG: PythonCall
+          JULIA_NUM_THREADS: '2'
       - name: Process coverage
         uses: julia-actions/julia-processcoverage@v1
       - name: Upload coverage to Codecov
@@ -84,6 +85,8 @@ jobs:
       - name: Run tests
         run: |
           pytest -s --nbval --cov=pysrc ./pytest/
+        env:
+          PYTHON_JULIACALL_THREADS: '2'
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         env:

CondaPkg.toml

@@ -1,6 +1,9 @@
 [deps.libstdcxx-ng]
 version = "<=julia"
 
+[deps.openssl]
+version = "<=julia"
+
 [deps.python]
 build = "**cpython**"
 version = ">=3.8,<4"

Project.toml

@@ -1,7 +1,7 @@
 name = "PythonCall"
 uuid = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 authors = ["Christopher Doris <github.com/cjdoris>"]
-version = "0.9.20"
+version = "0.9.22"
 
 [deps]
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
@@ -18,7 +18,7 @@ UnsafePointers = "e17b2a0c-0bdf-430a-bd0c-3a23cae4ff39"
 
 [compat]
 Aqua = "0 - 999"
-CondaPkg = "0.2.21"
+CondaPkg = "0.2.23"
 Dates = "1"
 Libdl = "1"
 MacroTools = "0.5"

README.md

@@ -40,9 +40,8 @@ In this example we use the Python module JuliaCall from an IPython notebook to t
 
 ## What about PyCall?
 
-The existing package [PyCall](https://github.com/JuliaPy/PyCall.jl) is another similar interface to Python. Here we note some key differences, but a more detailed comparison is in the documentation.
+The existing package [PyCall](https://github.com/JuliaPy/PyCall.jl) is another similar interface to Python. Here we note some key differences:.
 - PythonCall supports a wider range of conversions between Julia and Python, and the conversion mechanism is extensible.
 - PythonCall by default never copies mutable objects when converting, but instead directly wraps the mutable object. This means that modifying the converted object modifies the original, and conversion is faster.
 - PythonCall does not usually automatically convert results to Julia values, but leaves them as Python objects. This makes it easier to do Pythonic things with these objects (e.g. accessing methods) and is type-stable.
-- PythonCall installs dependencies into a separate Conda environment for each Julia project. This means each Julia project can have an isolated set of Python dependencies.
-- PythonCall supports Julia 1.6.1+ and Python 3.8+ whereas PyCall supports Julia 0.7+ and Python 2.7+.
+- PythonCall installs dependencies into a separate Conda environment for each Julia project using [CondaPkg](https://github.com/JuliaPy/CondaPkg.jl). This means each Julia project can have an isolated set of Python dependencies.

bump.jl

@@ -9,7 +9,7 @@ function bump(file, oldpat, newpat)
     oldtext = read(file, String)
     newtext = replace(oldtext, oldpat => newpat)
     @assert newtext != oldtext
-    write(file, newtext)    
+    write(file, newtext)
 end
 
 function bumpver(file, pattern, oldver, newver)

docs/customdocs.jl

@@ -53,8 +53,8 @@ function runner(::Type{CustomDocExpander}, node, page, doc)
         Dict{Symbol,Any}(    # NOTE: Not sure about what to put here.                            
             :module => Main, # This is supposed to be tracking python code.
             :path => "",
-            :linenumber => 0
-        )
+            :linenumber => 0,
+        ),
     )::Docs.DocStr
 
     # NOTE: This was modified because the original Documenter.create_docsnode was generating unreachable links
@@ -80,12 +80,10 @@ function _parse_docs(code::AbstractString)
     m = match(r"^(.+?)\s*-\s*(.+?)\s*(\n[\s\S]*)$", strip(code))
 
     if isnothing(m)
-        error(
-            """
-            Invalid docstring:
-            $(code)
-            """
-        )
+        error("""
+              Invalid docstring:
+              $(code)
+              """)
     end
 
     name = Symbol(m[1])
@@ -134,4 +132,4 @@ function _create_docsnode(docstring, result, object, page, doc)
     return MarkdownAST.Node(docsnode)
 end
 
-end # module CustomDocs
+end # module CustomDocs

docs/make.jl

@@ -5,32 +5,22 @@ include("customdocs.jl")
 makedocs(
     sitename = "PythonCall & JuliaCall",
     modules = [PythonCall],
-    format = Documenter.HTML(
-        assets = ["assets/favicon.ico"],
-    ),
+    format = Documenter.HTML(assets = ["assets/favicon.ico"]),
     warnonly = [:missing_docs], # avoid raising error when docs are missing
     pages = [
         "Home" => "index.md",
-        "The Julia module PythonCall" => [
-            "Guide" => "pythoncall.md",
-            "Reference" => "pythoncall-reference.md",
-        ],
-        "The Python module JuliaCall" => [
-            "Guide" => "juliacall.md",
-            "Reference" => "juliacall-reference.md",
-        ],
+        "The Julia module PythonCall" =>
+            ["Guide" => "pythoncall.md", "Reference" => "pythoncall-reference.md"],
+        "The Python module JuliaCall" =>
+            ["Guide" => "juliacall.md", "Reference" => "juliacall-reference.md"],
         "Conversion" => [
             "Julia to Python" => "conversion-to-python.md",
             "Python to Julia" => "conversion-to-julia.md",
         ],
         "compat.md",
         "faq.md",
-        "pycall.md",
         "releasenotes.md",
-    ]
+    ],
 )
 
-deploydocs(
-    repo = raw"github.com/JuliaPy/PythonCall.jl.git",
-    push_preview = true
-)
+deploydocs(repo = raw"github.com/JuliaPy/PythonCall.jl.git", push_preview = true)