From 6337d6e7b06b8f6462f952e16e2e2773b3291045 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Thu, 15 Aug 2024 12:37:50 +1000
Subject: [PATCH 01/15] Add conda packaging and deployment to accessnri channel

---
 .gitattributes           |   1 +
 .github/workflows/CD.yml |  40 +++
 .pylintrc                |   5 +
 conda/environment.yml    |  13 +
 conda/meta.yml           |  49 +++
 pyproject.toml           |  46 +++
 setup.py                 |   7 +
 umpost/_version.py       | 683 +++++++++++++++++++++++++++++++++++++++
 8 files changed, 844 insertions(+)
 create mode 100644 .gitattributes
 create mode 100644 .github/workflows/CD.yml
 create mode 100644 .pylintrc
 create mode 100644 conda/environment.yml
 create mode 100644 conda/meta.yml
 create mode 100644 pyproject.toml
 create mode 100644 setup.py
 create mode 100644 umpost/_version.py

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..66ce36e
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+umpost/_version.py export-subst
diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
new file mode 100644
index 0000000..af7580a
--- /dev/null
+++ b/.github/workflows/CD.yml
@@ -0,0 +1,40 @@
+name: CD
+
+on:
+  push:
+    branches:
+        - master
+
+env:
+  PY_VERSION: 3.10
+
+jobs:
+
+  conda:
+    name: Build with conda and upload
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+            fetch-tags: true
+            fetch-depth: 0 
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ env.PY_VERSION }}
+          environment-file: conda/environment.yml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Build and upload the conda package
+        uses: uibcdf/action-build-and-upload-conda-packages@c6e7a90ad5e599d6cde76e130db4ee52ad733ecf
+        with:
+          meta_yaml_dir: conda
+          python-version: ${{ env.PY_VERSION }}
+          user: accessnri
+          label: main
+          token: ${{ secrets.anaconda_token }}
\ No newline at end of file
diff --git a/.pylintrc b/.pylintrc
new file mode 100644
index 0000000..b63bb64
--- /dev/null
+++ b/.pylintrc
@@ -0,0 +1,5 @@
+[MAIN]
+
+# Files or directories to be skipped. They should be base names, not
+# paths.
+ignore=_version.py
diff --git a/conda/environment.yml b/conda/environment.yml
new file mode 100644
index 0000000..0667bea
--- /dev/null
+++ b/conda/environment.yml
@@ -0,0 +1,13 @@
+name: um2nc
+
+channels:
+    - conda-forge
+    - accessnri
+    - coecms
+    - defaults
+
+dependencies:
+    - anaconda-client
+    - conda-build
+    - conda-verify
+    - versioneer
diff --git a/conda/meta.yml b/conda/meta.yml
new file mode 100644
index 0000000..b8a1c53
--- /dev/null
+++ b/conda/meta.yml
@@ -0,0 +1,49 @@
+{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %}
+{% set version = data.get('version') %}
+{% set pyproj = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set project = pyproj.get('project') %}
+
+package:
+    name: um2nc
+    version: "{{ version }}"
+
+build:
+    noarch: python
+    number: 0
+    script: "{{ python }} -m pip install . -vv"
+    entry_points:
+        {% for name, script in project.get('scripts', {}).items() %}
+        - {{ name }} = {{ script }}
+        {% endfor %}
+
+source:
+    path: ../
+
+requirements:
+    host:
+        - python
+        - pip
+        - setupools >=61.0.0
+        - versioneer
+    run:
+        - python >=3.10
+        {% for dep in project.get('dependencies', []) %}
+        - {{ dep }}
+        {% endfor %}
+
+test:
+    imports:
+        - umpost
+    requires:
+        - pytest
+    source_files:
+        - test/**
+    commands:
+        - py.test
+
+about:
+    home: https://github.com/access-nri/um2nc-standalone
+    license: Apache Software
+    license_family: Apache
+    summary: "Tool to convert fieldsfiles into netCDF format. Used for post-processing UM climate model output"
+
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..1d79007
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,46 @@
+[project]
+name = "um2nc"
+authors = [
+  {name = "Ben Davies", email="ben.davies@anu.edu.au"},
+  {name = "Martin Dix", email="martin.dix@anu.edu.au"},
+  {name = "Spencer Wong", email="spencer.wong@anu.edu.au"},
+]
+maintainers = [
+    { name = "ACCESS-NRI", email = "access.nri@anu.edu.au" }
+]
+description = "Program to convert Unified Model output files in fields file format to netCDF"
+license = { text = "Apache-2.0" }
+readme = "README.md"
+keywords = ["netCDF", "UM", "postprocessing"]
+dynamic = ["version"]
+dependencies = [
+  "numpy",
+  "mule",
+  "cftime",
+  "netCDF4",
+  "scitools-iris",
+  "cf-units",
+  "PyYAML",
+  "f90nml",
+]
+[project.scripts]
+um2nc = "umpost.um2netcdf:main"
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "umpost/_version.py"
+versionfile_build = "umpost/_version.py"
+tag_prefix = ""
+parentdir_prefix = "umpost-"
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools>64", 
+    "versioneer[toml]"
+]
+
+[tool.setuptools.packages.find]
+include = ["umpost*"]
+namespaces = false
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..9ed5e21
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,7 @@
+from setuptools import setup
+import versioneer
+
+setup(
+    version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
+)
diff --git a/umpost/_version.py b/umpost/_version.py
new file mode 100644
index 0000000..1fef369
--- /dev/null
+++ b/umpost/_version.py
@@ -0,0 +1,683 @@
+
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain.
+# Generated by versioneer-0.29
+# https://github.com/python-versioneer/python-versioneer
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+from typing import Any, Callable, Dict, List, Optional, Tuple
+import functools
+
+
+def get_keywords() -> Dict[str, str]:
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "$Format:%d$"
+    git_full = "$Format:%H$"
+    git_date = "$Format:%ci$"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+    VCS: str
+    style: str
+    tag_prefix: str
+    parentdir_prefix: str
+    versionfile_source: str
+    verbose: bool
+
+
+def get_config() -> VersioneerConfig:
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "pep440"
+    cfg.tag_prefix = ""
+    cfg.parentdir_prefix = "umpost-"
+    cfg.versionfile_source = "umpost/_version.py"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
+
+
+def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
+    """Create decorator to mark a method as the handler of a VCS."""
+    def decorate(f: Callable) -> Callable:
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(
+    commands: List[str],
+    args: List[str],
+    cwd: Optional[str] = None,
+    verbose: bool = False,
+    hide_stderr: bool = False,
+    env: Optional[Dict[str, str]] = None,
+) -> Tuple[Optional[str], Optional[int]]:
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    process = None
+
+    popen_kwargs: Dict[str, Any] = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
+    for command in commands:
+        try:
+            dispcmd = str([command] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None), **popen_kwargs)
+            break
+        except OSError as e:
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, process.returncode
+    return stdout, process.returncode
+
+
+def versions_from_parentdir(
+    parentdir_prefix: str,
+    root: str,
+    verbose: bool,
+) -> Dict[str, Any]:
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for _ in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords: Dict[str, str] = {}
+    try:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(
+    keywords: Dict[str, str],
+    tag_prefix: str,
+    verbose: bool,
+) -> Dict[str, Any]:
+    """Get version information from git keywords."""
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
+    date = keywords.get("date")
+    if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = {r for r in refs if re.search(r'\d', r)}
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
+            if verbose:
+                print("picking %s" % r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(
+    tag_prefix: str,
+    root: str,
+    verbose: bool,
+    runner: Callable = run_command
+) -> Dict[str, Any]:
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
+
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=not verbose)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = runner(GITS, [
+        "describe", "--tags", "--dirty", "--always", "--long",
+        "--match", f"{tag_prefix}[[:digit:]]*"
+    ], cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces: Dict[str, Any] = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparsable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root)
+        pieces["distance"] = len(out.split())  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces: Dict[str, Any]) -> str:
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces: Dict[str, Any]) -> str:
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
+
+    Exceptions:
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        if pieces["distance"]:
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
+    else:
+        # exception #1
+        rendered = "0.post0.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_old(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces: Dict[str, Any]) -> str:
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces: Dict[str, Any]) -> str:
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions() -> Dict[str, Any]:
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for _ in cfg.versionfile_source.split('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}

From 203ad187ce4ac3300c2f15fa2deb5c916e6e0143 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Thu, 15 Aug 2024 13:56:52 +1000
Subject: [PATCH 02/15] Add Apache 2.0 license file

Change CI to deploy on tagging.

Change to modern pytest invocation.

Added in change to license in conda metadata
---
 .github/workflows/CD.yml |   6 +-
 LICENSE                  | 201 +++++++++++++++++++++++++++++++++++++++
 conda/meta.yml           |   1 +
 pyproject.toml           |   2 +-
 4 files changed, 206 insertions(+), 4 deletions(-)
 create mode 100644 LICENSE

diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
index af7580a..b9e2312 100644
--- a/.github/workflows/CD.yml
+++ b/.github/workflows/CD.yml
@@ -1,9 +1,9 @@
 name: CD
 
 on:
-  push:
-    branches:
-        - master
+    push:
+      tags:
+        - '*'
 
 env:
   PY_VERSION: 3.10
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..261eeb9
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
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+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
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+      designated in writing by the copyright owner as "Not a Contribution."
+
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+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
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+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
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+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
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+      Contribution(s) alone or by combination of their Contribution(s)
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+      institute patent litigation against any entity (including a
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+      or a Contribution incorporated within the Work constitutes direct
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+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
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+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
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+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
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+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
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+      Work (including but not limited to damages for loss of goodwill,
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+   9. Accepting Warranty or Additional Liability. While redistributing
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+      and charge a fee for, acceptance of support, warranty, indemnity,
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+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+      file or class name and description of purpose be included on the
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+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
diff --git a/conda/meta.yml b/conda/meta.yml
index b8a1c53..ce5dcd9 100644
--- a/conda/meta.yml
+++ b/conda/meta.yml
@@ -44,6 +44,7 @@ test:
 about:
     home: https://github.com/access-nri/um2nc-standalone
     license: Apache Software
+    license_file: LICENSE
     license_family: Apache
     summary: "Tool to convert fieldsfiles into netCDF format. Used for post-processing UM climate model output"
 
diff --git a/pyproject.toml b/pyproject.toml
index 1d79007..ac65337 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ maintainers = [
     { name = "ACCESS-NRI", email = "access.nri@anu.edu.au" }
 ]
 description = "Program to convert Unified Model output files in fields file format to netCDF"
-license = { text = "Apache-2.0" }
+license = { file = "LICENSE" }
 readme = "README.md"
 keywords = ["netCDF", "UM", "postprocessing"]
 dynamic = ["version"]

From 598cebcdd97ada12a9db2e64270e64b4073b4aa5 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Thu, 15 Aug 2024 14:56:19 +1000
Subject: [PATCH 03/15] Add CI workflow Quote python version string

---
 .github/workflows/CD.yml |  2 +-
 .github/workflows/CI.yml | 82 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 83 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/CI.yml

diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
index b9e2312..d60146b 100644
--- a/.github/workflows/CD.yml
+++ b/.github/workflows/CD.yml
@@ -6,7 +6,7 @@ on:
         - '*'
 
 env:
-  PY_VERSION: 3.10
+  PY_VERSION: "3.10"
 
 jobs:
 
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
new file mode 100644
index 0000000..984ba94
--- /dev/null
+++ b/.github/workflows/CI.yml
@@ -0,0 +1,82 @@
+# Run CI tests
+name: CI
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ master, develop ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  PY_VERSION: "3.10"
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  conda-build:
+    name: Conda Build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ env.PY_VERSION }}
+          environment-file: conda/environment.yml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Run conda build
+        shell: bash -el {0}
+        run: conda build . --no-anaconda-upload
+
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+
+    # Run the job for different versions of python
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+
+      - name: Checkout code
+        uses: actions/checkout@v4.1.7
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install source
+        shell: bash -l {0}
+        run: python -m pip install -e .
+
+      - name: List installed packages
+        shell: bash -l {0}
+        run: conda list
+
+      - name: Lint
+        run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=backports -E umpost
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: python -m pytest --cov=umpost --cov-report=xml -s test
+
+      - name: Upload code coverage
+        uses: codecov/codecov-action@v4
+        # Only upload once for the installed version
+        if: matrix.python-version == ${{ env.PY_VERSION }}
+        with:
+          token: ${{ secrets.codecov_token }}
+          files: ./coverage.xml
\ No newline at end of file

From e8b2b00f69953f248a70b254c402410c464e20e7 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 11:21:43 +1000
Subject: [PATCH 04/15] Move meta.yml to meta.yaml, and fixed extraction of
 project name from pyproject.toml Replace python interpreter with plain text

---
 conda/{meta.yml => meta.yaml} | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)
 rename conda/{meta.yml => meta.yaml} (87%)

diff --git a/conda/meta.yml b/conda/meta.yaml
similarity index 87%
rename from conda/meta.yml
rename to conda/meta.yaml
index ce5dcd9..86aa42a 100644
--- a/conda/meta.yml
+++ b/conda/meta.yaml
@@ -2,15 +2,16 @@
 {% set version = data.get('version') %}
 {% set pyproj = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
 {% set project = pyproj.get('project') %}
+{% set name = project.get('name') %}
 
 package:
-    name: um2nc
+    name: {{ name }}
     version: "{{ version }}"
 
 build:
     noarch: python
     number: 0
-    script: "{{ python }} -m pip install . -vv"
+    script: "python3 -m pip install . -vv"
     entry_points:
         {% for name, script in project.get('scripts', {}).items() %}
         - {{ name }} = {{ script }}
@@ -23,7 +24,7 @@ requirements:
     host:
         - python
         - pip
-        - setupools >=61.0.0
+        - setuptools >=61.0.0
         - versioneer
     run:
         - python >=3.10
@@ -39,7 +40,7 @@ test:
     source_files:
         - test/**
     commands:
-        - py.test
+        - pytest
 
 about:
     home: https://github.com/access-nri/um2nc-standalone

From e8aab36cde68a867638fbd3e78fd3245564c6700 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 11:44:42 +1000
Subject: [PATCH 05/15] Remove test section from conda metadata

---
 conda/meta.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index 86aa42a..a32554a 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -32,16 +32,6 @@ requirements:
         - {{ dep }}
         {% endfor %}
 
-test:
-    imports:
-        - umpost
-    requires:
-        - pytest
-    source_files:
-        - test/**
-    commands:
-        - pytest
-
 about:
     home: https://github.com/access-nri/um2nc-standalone
     license: Apache Software

From 0e39df9f68bb81a28486247aa87420dbdb36349b Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 12:31:43 +1000
Subject: [PATCH 06/15] Reuse conda build artifact in CI testing workflow

---
 .github/workflows/CI.yml | 30 +++++++++++++++++++++++++++---
 conda/environment.yml    |  1 +
 2 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 984ba94..343e8f4 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -20,6 +20,10 @@ jobs:
   conda-build:
     name: Conda Build
     runs-on: ubuntu-latest
+    env:
+      NAME: test-${{ github.event.repository.name }}
+    outputs:
+      artifact-name: ${{ env.NAME }}
     steps:
       - uses: actions/checkout@v4
 
@@ -35,32 +39,52 @@ jobs:
 
       - name: Run conda build
         shell: bash -el {0}
-        run: conda build . --no-anaconda-upload
+        run: |
+          conda build . --no-anaconda-upload --output-folder=./build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ${{ env.NAME }}
+          if-no-files-found: error
+          path: ./build
 
   tests:
     name: Tests
     runs-on: ubuntu-latest
+    needs: conda-build
 
     # Run the job for different versions of python
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
 
+    env:
+      ARTIFACT_LOCATION: ${{ github.workspace }}/conda-local
+
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
 
       - name: Checkout code
         uses: actions/checkout@v4.1.7
 
+      - uses: actions/download-artifact@v4
+        with:
+          name: ${{ needs.conda-build.outputs.artifact-name }}
+          path: ${{ env.ARTIFACT_LOCATION }}
+
       - name: Setup conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           python-version: ${{ matrix.python-version }}
 
-      - name: Install source
+      - name: DEBUG - where are things
+        run: ls ${{ env.ARTIFACT_LOCATION }}
+
+      - name: Install conda package
         shell: bash -l {0}
-        run: python -m pip install -e .
+        run: |
+          conda install -c file://${{ env.ARTIFACT_LOCATION }} um2nc
 
       - name: List installed packages
         shell: bash -l {0}
diff --git a/conda/environment.yml b/conda/environment.yml
index 0667bea..df43c50 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -11,3 +11,4 @@ dependencies:
     - conda-build
     - conda-verify
     - versioneer
+    - pylint

From d94d2463416dd883dbc4ba1ef4e855cc5a9c0a60 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 13:34:45 +1000
Subject: [PATCH 07/15] Add channels to um2nc install

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 343e8f4..b199a59 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -84,7 +84,7 @@ jobs:
       - name: Install conda package
         shell: bash -l {0}
         run: |
-          conda install -c file://${{ env.ARTIFACT_LOCATION }} um2nc
+          conda install -c conda-forge -c accessnri -c coecms -c file://${{ env.ARTIFACT_LOCATION }} um2nc
 
       - name: List installed packages
         shell: bash -l {0}

From e9b87ecd852c9a14c27d6fc86b4cd6d6a9b72d66 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 13:47:25 +1000
Subject: [PATCH 08/15] Use environment file to ensure pylint is installed

---
 .github/workflows/CI.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b199a59..c01bcc6 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -77,6 +77,8 @@ jobs:
         with:
           miniconda-version: "latest"
           python-version: ${{ matrix.python-version }}
+          environment-file: conda/environment.yml
+          activate-environment: um2nc
 
       - name: DEBUG - where are things
         run: ls ${{ env.ARTIFACT_LOCATION }}

From f394c51fc976bdd2e7ec04c5ec03949a40a21108 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 13:56:16 +1000
Subject: [PATCH 09/15] Add explicit bash shell to linting step to use
 activated conda env correctly

---
 .github/workflows/CI.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c01bcc6..6ab6534 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -93,6 +93,7 @@ jobs:
         run: conda list
 
       - name: Lint
+        shell: bash -l {0}
         run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=backports -E umpost
 
       - name: Run tests

From e998ccef7a870d36450e88ec5f375052fb8636f9 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Fri, 16 Aug 2024 16:03:35 +1000
Subject: [PATCH 10/15] Ignore um2netcdf imports in pyline Add pytest and
 pytest-cov to test environment

---
 .github/workflows/CI.yml | 2 +-
 conda/environment.yml    | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 6ab6534..0eb90fd 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -94,7 +94,7 @@ jobs:
 
       - name: Lint
         shell: bash -l {0}
-        run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=backports -E umpost
+        run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=um2netcdf4,umpost -E umpost
 
       - name: Run tests
         shell: bash -l {0}
diff --git a/conda/environment.yml b/conda/environment.yml
index df43c50..87cf5b4 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -12,3 +12,5 @@ dependencies:
     - conda-verify
     - versioneer
     - pylint
+    - pytest
+    - pytest-cov

From 0e5907bdc4b9d4465913cd3609a394e07be1138f Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Mon, 19 Aug 2024 16:24:34 +1000
Subject: [PATCH 11/15] Change to trigger branch from master to main

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0eb90fd..2bd67d2 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -5,9 +5,9 @@ name: CI
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
-    branches: [ master, develop ]
+    branches: [ main, develop ]
   pull_request:
-    branches: [ master, develop ]
+    branches: [ main, develop ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:

From 4160b63a23d9716ad04c869c57303d151841c66c Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Mon, 19 Aug 2024 16:31:29 +1000
Subject: [PATCH 12/15] Add EOF endings to CI and CD workflow files

---
 .github/workflows/CD.yml | 2 +-
 .github/workflows/CI.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
index d60146b..ea89ab4 100644
--- a/.github/workflows/CD.yml
+++ b/.github/workflows/CD.yml
@@ -37,4 +37,4 @@ jobs:
           python-version: ${{ env.PY_VERSION }}
           user: accessnri
           label: main
-          token: ${{ secrets.anaconda_token }}
\ No newline at end of file
+          token: ${{ secrets.anaconda_token }}
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 2bd67d2..48df057 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -106,4 +106,4 @@ jobs:
         if: matrix.python-version == ${{ env.PY_VERSION }}
         with:
           token: ${{ secrets.codecov_token }}
-          files: ./coverage.xml
\ No newline at end of file
+          files: ./coverage.xml

From 02a7a7b99bf712049091e5a95dfe38563bc6d73f Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Tue, 20 Aug 2024 10:14:34 +1000
Subject: [PATCH 13/15] Add entrypoint test to CI

---
 .github/workflows/CI.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 48df057..2f93d2d 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -96,6 +96,10 @@ jobs:
         shell: bash -l {0}
         run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=um2netcdf4,umpost -E umpost
 
+      - name: Entrypoint test
+        shell: bash -l {0}
+        run: um2nc --help
+
       - name: Run tests
         shell: bash -l {0}
         run: python -m pytest --cov=umpost --cov-report=xml -s test

From 0e246cc50fd25e58eea4f78f2853d2e53612632d Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Tue, 20 Aug 2024 10:26:34 +1000
Subject: [PATCH 14/15] Prepend um2nc module name to entrypoint

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ac65337..76fef38 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   "f90nml",
 ]
 [project.scripts]
-um2nc = "umpost.um2netcdf:main"
+um2nc = "um2nc.umpost.um2netcdf:main"
 
 [tool.versioneer]
 VCS = "git"

From 2c7b35542072907613767526090108c4f67183f7 Mon Sep 17 00:00:00 2001
From: Aidan Heerdegen <aidan.heerdegen@anu.edu.au>
Date: Tue, 20 Aug 2024 12:41:16 +1000
Subject: [PATCH 15/15] Remove entrypoints and associated CI test, and
 debugging CI step

---
 .github/workflows/CI.yml | 7 -------
 pyproject.toml           | 2 --
 2 files changed, 9 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 2f93d2d..8a245ea 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -80,9 +80,6 @@ jobs:
           environment-file: conda/environment.yml
           activate-environment: um2nc
 
-      - name: DEBUG - where are things
-        run: ls ${{ env.ARTIFACT_LOCATION }}
-
       - name: Install conda package
         shell: bash -l {0}
         run: |
@@ -96,10 +93,6 @@ jobs:
         shell: bash -l {0}
         run: pylint --extension-pkg-whitelist=netCDF4 --ignored-modules=um2netcdf4,umpost -E umpost
 
-      - name: Entrypoint test
-        shell: bash -l {0}
-        run: um2nc --help
-
       - name: Run tests
         shell: bash -l {0}
         run: python -m pytest --cov=umpost --cov-report=xml -s test
diff --git a/pyproject.toml b/pyproject.toml
index 76fef38..bfda3c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,8 +23,6 @@ dependencies = [
   "PyYAML",
   "f90nml",
 ]
-[project.scripts]
-um2nc = "um2nc.umpost.um2netcdf:main"
 
 [tool.versioneer]
 VCS = "git"