Update project dependencies

.devcontainer/devcontainer.json

@@ -1,26 +1,35 @@
 {
     "name": "fmflow",
-    "build": {
-        "context": "..",
-        "dockerfile": "Dockerfile"
+    "image":"python:3.12",
+    "containerEnv": {
+        "POETRY_VIRTUALENVS_CREATE": "false"
     },
-    "postCreateCommand": "poetry install",
-    "extensions": [
-        "github.vscode-pull-request-github",
-        "mhutchie.git-graph",
-        "ms-python.python",
-        "streetsidesoftware.code-spell-checker",
-        "tamasfe.even-better-toml"
+    "runArgs": [
+        "--name=fmflow"
     ],
-    "settings": {
-        "files.insertFinalNewline": true,
-        "files.trimTrailingWhitespace": true,
-        "python.formatting.provider": "black",
-        "python.languageServer": "Pylance",
-        "[python]": {
-            "editor.formatOnSave": true,
-            "editor.insertSpaces": true,
-            "editor.tabSize": 4
+    "onCreateCommand": "pip install poetry==1.8.5",
+    "postCreateCommand": "poetry install",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "github.vscode-pull-request-github",
+                "mhutchie.git-graph",
+                "ms-python.black-formatter",
+                "ms-python.python",
+                "streetsidesoftware.code-spell-checker",
+                "tamasfe.even-better-toml"
+            ],
+            "settings": {
+                "files.insertFinalNewline": true,
+                "files.trimTrailingWhitespace": true,
+                "[python]": {
+                    "editor.defaultFormatter": "ms-python.black-formatter",
+                    "editor.formatOnSave": true,
+                    "editor.insertSpaces": true,
+                    "editor.tabSize": 4,
+                    "python.languageServer": "Pylance"
+                }
+            }
         }
     }
 }

.github/workflows/gh-pages.yml → .github/workflows/gh-pages.yaml

@@ -12,16 +12,16 @@ jobs:
     env:
       POETRY_VIRTUALENVS_CREATE: false
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-      - name: Install project dependencies
-        run: pip install poetry && poetry install
-      - name: Build docs
-        run: docs/build
-      - name: Deploy docs
-        uses: peaceiris/actions-gh-pages@v3
+          python-version: "3.12
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry install
+      - run: docs/build
+      - uses: peaceiris/actions-gh-pages@v3
         with:
           force_orphan: true
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pypi.yaml

@@ -0,0 +1,22 @@
+name: PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  job:
+    name: PyPI
+    runs-on: ubuntu-latest
+    env:
+      POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry publish --build

.github/workflows/tests.yaml

@@ -0,0 +1,34 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  job:
+    name: Test (Python ${{ matrix.python }})
+    runs-on: ubuntu-latest
+    env:
+      POETRY_VIRTUALENVS_CREATE: false
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry install
+      - run: black --check docs fmflow tests
+      - run: pytest -v tests
+      - run: docs/build

CITATION.cff

@@ -3,13 +3,13 @@ message: "If you use this software, please cite it as below."
 
 title: "fmflow"
 abstract: "Data analysis package for FMLO"
-version: 0.4.0
-date-released: 2022-09-09
+version: 0.5.0
+date-released: 2025-03-19
 license: "MIT"
 doi: "10.5281/zenodo.3433962"
 url: "https://github.com/fmlo-dev/fmflow"
 authors:
   - given-names: "Akio"
     family-names: "Taniguchi"
-    affiliation: "Nagoya University"
+    affiliation: "Kitami Institute of Technology"
     orcid: "https://orcid.org/0000-0002-9695-6183"

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2022 Akio Taniguchi
+Copyright (c) 2017-2025 Akio Taniguchi
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -4,6 +4,6 @@
 [![Python](https://img.shields.io/pypi/pyversions/fmflow?label=Python&color=cornflowerblue&style=flat-square)](https://pypi.org/project/fmflow/)
 [![Downloads](https://img.shields.io/pypi/dm/fmflow?label=Downloads&color=cornflowerblue&style=flat-square)](https://pepy.tech/project/fmflow)
 [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3433962-cornflowerblue?style=flat-square)](https://doi.org/10.5281/zenodo.3433962)
-[![Tests](https://img.shields.io/github/workflow/status/fmlo-dev/fmflow/Tests?label=Tests&style=flat-square)](https://github.com/fmlo-dev/fmflow/actions)
+[![Tests](https://img.shields.io/github/actions/workflow/status/fmlo-dev/fmflow/tests.yaml?label=Tests&style=flat-square)](https://github.com/fmlo-dev/fmflow/actions)
 
 Data analysis package for FMLO

fmflow/__init__.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 __author__ = "Akio Taniguchi"
 
 from . import utils

fmflow/fits/aste/functions.py

@@ -91,7 +91,7 @@ def read_fmlolog(fmlolog):
     fmlolog = Path(fmlolog).expanduser()
 
     # read fmlolog
-    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -123,7 +123,7 @@ def read_antennalog(antennalog):
     antennalog = Path(antennalog).expanduser()
 
     # read antennalog
-    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -174,7 +174,7 @@ def check_backend(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
 
@@ -203,8 +203,8 @@ def read_backendlog_mac(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
-    mac = yaml.load(CONF_BACKEND_MAC, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
+    mac = yaml.load(CONF_BACKEND_MAC, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
     obs = fm.utils.CStructReader(mac["obs"], IGNORED_KEY, byteorder)
@@ -268,7 +268,7 @@ def eof(f):
             data["arraydata"][on] *= np.mean(data["dalpha"][on])
 
         ## apply ZERO and coeff. to R data
-        for (r, sky) in zip(rs, skys):
+        for r, sky in zip(rs, skys):
             data["arraydata"][r] -= data["arraydata"][zero]
             data["arraydata"][r] *= data["dbeta"][sky]
 
@@ -287,7 +287,7 @@ def eof(f):
     tforms = map(fm.utils.ctype_to_tform, ctypes, shapes)
     fmts = OrderedDict(item for item in zip(names, tforms))
 
-    num = re.findall("\d+", fmts.pop("iary_data"))[0]
+    num = re.findall(r"\d+", fmts.pop("iary_data"))[0]
     fmts["arraydata"] = "{}E".format(num)
     fmts["starttime"] = "A26"
     fmts["arrayid"] = fmts.pop("cary_name")
@@ -324,7 +324,7 @@ def make_obsinfo_mac(hdus):
     p = fm.utils.DatetimeParser()
     flag = np.array(obsinfo["iary_usefg"], dtype=bool)
 
-    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -339,7 +339,7 @@ def make_obsinfo_mac(hdus):
     header["object"] = obsinfo["cobj_name"]
     header["ra"] = obsinfo["dsrc_pos"][0][0]
     header["dec"] = obsinfo["dsrc_pos"][1][0]
-    header["equinox"] = float(re.findall("\d+", obsinfo["cepoch"])[0])
+    header["equinox"] = float(re.findall(r"\d+", obsinfo["cepoch"])[0])
 
     data = OrderedDict()
     data["arrayid"] = np.unique(datinfo["arrayid"])