From 67b04bc460d0f873aa936625c5a4e430738675f9 Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Thu, 5 May 2022 14:39:48 +0200
Subject: [PATCH 1/6] Bump ixmp dependency to 3.5.0 in setup.cfg

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index ce8bf08ab..2a0dcc927 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -33,7 +33,7 @@ zip_safe = True
 include_package_data = True
 install_requires =
     click
-    ixmp >= 3.4.0
+    ixmp >= 3.5.0
     numpy
     pandas >= 1.2
     PyYAML

From 3648369c628c91a3612abf20bb69b40575e1b216 Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Thu, 5 May 2022 14:43:57 +0200
Subject: [PATCH 2/6] Mark v3.5.0 in release notes

---
 RELEASE_NOTES.rst | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/RELEASE_NOTES.rst b/RELEASE_NOTES.rst
index f391fa176..b891ec4fc 100644
--- a/RELEASE_NOTES.rst
+++ b/RELEASE_NOTES.rst
@@ -1,5 +1,13 @@
-Next release
-============
+.. Next release
+.. ============
+
+.. All changes
+.. -----------
+
+.. _v3.5.0:
+
+v3.5.0 (2022-05-06)
+===================
 
 Migration notes
 ---------------

From b164d3de78a3fa7d2a45d493672d4c295d64046f Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Thu, 5 May 2022 16:43:17 +0200
Subject: [PATCH 3/6] Move tool config for isort, mypy, pytest to
 pyproject.toml

---
 pyproject.toml | 38 +++++++++++++++++++++++++++++++++
 setup.cfg      | 58 --------------------------------------------------
 2 files changed, 38 insertions(+), 58 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..15bc81c36
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+
+[tool.isort]
+profile = "black"
+
+[[tool.mypy.overrides]]
+# Packages/modules for which no type hints are available.
+module = [
+  "asyncssh",
+  "matplotlib.*",
+  "numpy",
+  "pandas.*",
+  "pint",
+  "pyam",
+  "pytest",
+  "setuptools",
+  "xarray",
+  # Indirectly via ixmp; this should be a subset of the list in ixmp's setup.cfg
+  "dask",
+  "jpype",
+  "nbclient",
+  "nbformat",
+  "memory_profiler",
+  "sparse",
+]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+# Disable faulthandler plugin on Windows to prevent spurious console noise
+addopts = """
+  --cov=message_ix --cov-report=
+  -m "not nightly and not rmessageix"
+  -p no:faulthandler"""
+markers = [
+  "nightly: Slow-running nightly tests of particular scenarios.",
+  "rmessageix: test of the message_ix R interface.",
+]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index 2a0dcc927..c9e67f176 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,7 +26,6 @@ classifiers =
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Information Analysis
 
-
 [options]
 packages = message_ix
 zip_safe = True
@@ -65,72 +64,15 @@ tests =
     pytest-cov
     requests
 
-
 [options.entry_points]
 console_scripts =
     message-ix = message_ix.cli:main
 
-[tool:pytest]
-# Disable faulthandler plugin on Windows to prevent spurious console noise
-addopts = --cov=message_ix --cov-report=
-    -m "not nightly and not rmessageix"
-    -p no:faulthandler
-markers =
-    nightly: Slow-running nightly tests of particular scenarios.
-    rmessageix: test of the message_ix R interface.
-
 [codecov.run]
 omit =
     message_ix/model/*
     message_ix/tests/test_nightly.py
     message_ix/testing/nightly.py
 
-[aliases]
-test = pytest
-
-[isort]
-force_grid_wrap = 0
-include_trailing_comma = True
-line_length = 88
-multi_line_output = 3
-use_parentheses = True
-
 [flake8]
 max-line-length = 88
-
-[mypy]
-# Empty section required as of mypy 0.800;
-# see https://github.com/python/mypy/issues/9940
-
-[mypy-asyncssh.*]
-ignore_missing_imports = True
-[mypy-matplotlib.*]
-ignore_missing_imports = True
-[mypy-numpy.*]
-ignore_missing_imports = True
-[mypy-pandas.*]
-ignore_missing_imports = True
-[mypy-pint.*]
-ignore_missing_imports = True
-[mypy-pyam.*]
-ignore_missing_imports = True
-[mypy-pytest.*]
-ignore_missing_imports = True
-[mypy-setuptools.*]
-ignore_missing_imports = True
-[mypy-xarray.*]
-ignore_missing_imports = True
-
-# Indirectly via ixmp; this should be a subset of the list in ixmp's setup.cfg
-[mypy-dask.*]
-ignore_missing_imports = True
-[mypy-jpype.*]
-ignore_missing_imports = True
-[mypy-nbclient.*]
-ignore_missing_imports = True
-[mypy-nbformat.*]
-ignore_missing_imports = True
-[mypy-memory_profiler.*]
-ignore_missing_imports = True
-[mypy-sparse.*]
-ignore_missing_imports = True

From 3ddf927133454fc7945d32484a119403dd98b7ef Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Thu, 5 May 2022 16:45:02 +0200
Subject: [PATCH 4/6] Mirror setup.cfg content in pyproject.toml

---
 pyproject.toml | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 81 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 15bc81c36..846f3bba5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,87 @@
 [build-system]
 requires = ["setuptools", "setuptools-scm"]
 
+# Replacement for setup.cfg
+#
+# Support for this section is experimental in setuptools 61–62.1.0. This should
+# not be enabled until that support is stable.
+#
+# [project]
+# name = "message_ix"
+# description = "the MESSAGEix integrated assessment model"
+# authors = [
+#   { email = "message_ix@iiasa.ac.at" },
+#   { name = "IIASA Energy, Climate, and Environment (ECE) Program" }
+# ]
+# license = { text = "Apache" }
+# readme = { file = "README.md", content-type = "text/markdown" }
+# classifiers = [
+#     "Development Status :: 5 - Production/Stable",
+#     "Intended Audience :: Developers",
+#     "Intended Audience :: Science/Research",
+#     "License :: OSI Approved :: Apache Software License",
+#     "Natural Language :: English",
+#     "Operating System :: OS Independent",
+#     "Programming Language :: Python",
+#     "Programming Language :: Python :: 3",
+#     "Programming Language :: Python :: 3.7",
+#     "Programming Language :: Python :: 3.8",
+#     "Programming Language :: Python :: 3.9",
+#     "Programming Language :: Python :: 3.10",
+#     "Programming Language :: R",
+#     "Topic :: Scientific/Engineering",
+#     "Topic :: Scientific/Engineering :: Information Analysis"
+# ]
+# dependencies = [
+#   "click",
+#   "ixmp >= 3.5.0",
+#   "numpy",
+#   "pandas >= 1.2",
+#   "PyYAML",
+# ]
+# dynamic = ["version"]
+#
+# [project.urls]
+# documentation = "https://docs.messageix.org/"
+# repository = "http://github.com/iiasa/message_ix"
+#
+# [tool.setuptools]
+# zip-safe = true
+#
+# [project.optional-dependencies]
+# report = ["ixmp[report]"]
+# docs = [
+#   # Duplicated from above; see pypa/setuptools#3221
+#   "ixmp[report]",
+#   "numpydoc",
+#   "sphinx >= 4.0",
+#   "sphinx_rtd_theme",
+#   "sphinxcontrib-bibtex",
+# ]
+# tutorial = [
+#   "ixmp[report]",
+#   "jupyter",
+#   "matplotlib"
+# ]
+# test = [
+#   "ixmp[report]",
+#   "numpydoc",
+#   "sphinx >= 4.0",
+#   "sphinx_rtd_theme",
+#   "sphinxcontrib-bibtex",
+#   "jupyter",
+#   "matplotlib"
+#   "asyncssh"
+#   "pint"
+#   "pyam-iamc >= 0.6"
+#   "pytest >= 5"
+#   "pytest-cov"
+#   "requests"
+# ]
+#
+# [project.scripts]
+# ixmp = "message-ix = message_ix.cli:main"
+
 [tool.isort]
 profile = "black"
 

From 258523a33fcb668f5121d6cee7e65ca174e324aa Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Thu, 5 May 2022 16:46:31 +0200
Subject: [PATCH 5/6] Remove mypy exclusions

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 846f3bba5..fde24a7d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -90,20 +90,16 @@ profile = "black"
 module = [
   "asyncssh",
   "matplotlib.*",
-  "numpy",
   "pandas.*",
-  "pint",
   "pyam",
   "pytest",
   "setuptools",
-  "xarray",
   # Indirectly via ixmp; this should be a subset of the list in ixmp's setup.cfg
   "dask",
   "jpype",
   "nbclient",
   "nbformat",
   "memory_profiler",
-  "sparse",
 ]
 ignore_missing_imports = true
 

From b5a8aa7ad0f46d6fa174836f03feba962ce87627 Mon Sep 17 00:00:00 2001
From: Laura Wienpahl <57132039+LauWien@users.noreply.github.com>
Date: Fri, 6 May 2022 10:12:00 +0200
Subject: [PATCH 6/6] Explain #561, #591 in migration notes

---
 RELEASE_NOTES.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/RELEASE_NOTES.rst b/RELEASE_NOTES.rst
index b891ec4fc..7cd1613f8 100644
--- a/RELEASE_NOTES.rst
+++ b/RELEASE_NOTES.rst
@@ -15,6 +15,12 @@ Migration notes
 The format of input data files for MACRO calibration has been changed in :pull:`327`.
 Files compatible with v3.4.0 and earlier will not work with this version and should be updated; see details of the current data file format in the :doc:`documentation <macro>`.
 
+:pull:`561` corrected the model internal logic for handling zero values in the :ref:`capacity_factor <params-tech>` parameter.
+Before this change, the GAMS code inserted a ``capacity_factor`` value of 1.0 where such zero values appeared; now, zeros are preserved, so the technologies may be created (``CAP``) but none of their capacity will be usable at the
+:math:`(n, t, y^V, y, h)` where zero values appear.
+This is consistent with the general concept of a “capacity factor”: for instance, a solar photovoltaic technology for electricity generation may have a non-zero *capacity* with a *capacity factor* of 0 at :math:`h=\text{night}`.
+This may cause changes in model output for scenarios where such zero values appear; see :issue:`591` for discussion, including methods to check for and adjust/remove such values.
+
 All changes
 -----------