Bump dependency versions, fix some issues that cropped up

- Sphinx now 4.*
- Fixed finesse_sphinx to work with Sphinx 4
- Updated sphinxcontrib-bibtex to 2.2.* to remove need for version pinning < 2.*
- Most other packages pinned to their latest PyPI versions
- Requirements files now don't pin versions for non-production tools (docs, build, etc.)

docs/source/conf.py

@@ -44,16 +44,17 @@ copyright = u"1999 to {} by {}".format(
 
 
 import os, re
+
 # The full version, including alpha/beta/rc tags.
-release = re.sub('^v', '', os.popen('git describe --tags').read().strip())
+release = re.sub("^v", "", os.popen("git describe --tags").read().strip())
 # The short X.Y version.
 version = release
 
 # Or specify manually:
 # The short X.Y version
-#version = "3.0a1"
+# version = "3.0a1"
 # The full version, including alpha/beta/rc tags
-#release = "3.0a1"
+# release = "3.0a1"
 
 # -- General configuration ---------------------------------------------------
 
@@ -529,6 +530,11 @@ autosummary_generate = True
 # files.
 autosummary_generate_overwrite = False
 
+# -- Options for sphinxcontrib-bibtex extension ------------------------------
+
+bibtex_bibfiles = ["zbiblio/refs.bib"]
+bibtex_default_style = "unsrt"
+
 # -- Options for numpydoc extension ------------------------------------------
 
 try:

docs/source/zbiblio/index.rst

@@ -5,6 +5,4 @@
     Bibliography
     ============
 
-.. bibliography:: refs.bib
-    :cited:
-    :style: unsrt
+.. bibliography::

requirements-build.txt

-### NOTE See https://finesse.readthedocs.io/en/latest/developer/codeguide/requirements.html
+### NOTE See https://finesse.docs.ligo.org/finesse3/developer/codeguide/requirements.html
 
 # Core
 -r requirements.txt
 
-cython == 0.29.22
+cython == 0.29.23

requirements-dev.txt

-### NOTE See https://finesse.readthedocs.io/en/latest/developer/codeguide/requirements.html
+### NOTE See https://finesse.docs.ligo.org/finesse3/developer/codeguide/requirements.html
 
 # Core
 -r requirements.txt
@@ -13,8 +13,8 @@
 -r requirements-doc.txt
 
 # Extras
-black == 19.10b0
+black
 pre-commit
-pylint == 2.7.0
-flake8 == 3.8.4
-flake8-bugbear == 20.11.1
+pylint
+flake8
+flake8-bugbear

requirements-doc.txt

 # Requirements for building documentation
-### NOTE See https://finesse.readthedocs.io/en/latest/developer/codeguide/requirements.html
+### NOTE See https://finesse.docs.ligo.org/finesse3/developer/codeguide/requirements.html
 
-sphinx == 3.5.4
-sphinx_rtd_theme == 0.5.2
-sphinxcontrib-bibtex < 2.0.0  # Can't use v2 due to bug; see setup.py requirements for more info.
-sphinxcontrib-katex == 0.6.1
-sphinxcontrib-svg2pdfconverter >= 1.0.0
-sphinxcontrib-programoutput == 0.17
-jupyter-sphinx == 0.3.2
-numpydoc == 1.1.0
-reslate >= 0.54.0
+sphinx
+sphinx_rtd_theme
+sphinxcontrib-bibtex
+sphinxcontrib-katex
+sphinxcontrib-svg2pdfconverter
+sphinxcontrib-programoutput
+jupyter-sphinx
+numpydoc
+reslate

requirements-test.txt

 # Requirements for running tests
-### NOTE See https://finesse.readthedocs.io/en/latest/developer/codeguide/requirements.html
+### NOTE See https://finesse.docs.ligo.org/finesse3/developer/codeguide/requirements.html
 
-pytest >= 5.4.1
-pytest-cov >= 2.10.1
+pytest
+pytest-cov
 coverage == 4.5.4  # Can't use latest version due to Cython bug: https://github.com/cython/cython/issues/3515
-pycobertura >= 2.0.0
-Faker == 4.0.2
-hypothesis == 5.10.1
+pycobertura
+Faker
+hypothesis

requirements.txt

-### NOTE See https://finesse.readthedocs.io/en/latest/developer/codeguide/requirements.html
+### NOTE See https://finesse.docs.ligo.org/finesse3/developer/codeguide/requirements.html
 
-numpy >= 1.20.0 #1.19 causes a seg fault, 1.20 is not available on conda so we must specify it here, see #306
+numpy >= 1.20.0 # 1.19 causes a segfault, 1.20 is not available on conda so we must specify it here, see #306
 scipy >= 1.4.0
 matplotlib >= 3.0.0
 networkx >= 2.4

setup.py

@@ -246,10 +246,7 @@ EXTRAS = {
         # Documentation.
         "sphinx",
         "sphinx_rtd_theme",
-        # Can't use latest sphinxcontrib-bibtex version due to a dependency incompatibility as of
-        # 2020-12-14 (https://github.com/executablebooks/jupyter-book/issues/1137). The version
-        # pinning can be removed once Jupyter Book > 0.8.3 is released.
-        "sphinxcontrib-bibtex < 2.0.0",
+        "sphinxcontrib-bibtex",
         "sphinxcontrib-katex",
         "sphinxcontrib-svg2pdfconverter",
         "sphinxcontrib-programoutput",

src/finesse_sphinx/__init__.py

@@ -429,6 +429,9 @@ class KatDomain(Domain):
             (name, signature, instruction.description, self.env.docname, anchor, 0)
         )
 
+    def merge_domaindata(self, docnames, otherdata):
+        self.data["instructions"].extend(otherdata["instructions"])
+
 
 def setup(app):
     app.add_config_value(