Unify package settings

Author: chstan

conda/meta.yaml

@@ -1,6 +1,3 @@
-# full guide of options:
-# https://conda.io/docs/user-guide/tasks/build-packages/define-metadata.html
-
 # To see what comes out after this template is processed, run:
 #    conda-render ./conda/
 
@@ -17,62 +14,63 @@ source:
   url: ../dist/{{ data.name }}-{{ data.version }}.tar.gz
 
 build:
-  number: 1
+  number: 2
   noarch: python
-  script: "python setup.py install --single-version-externally-managed --record=record.txt"
+  script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
 
-# unlike pypi, conda has a slightly different format for required
-# versions, with one space between package name and version specifier, i.e.
-# we must use - xarray >=0.9.6. For details see:
-# https://conda.io/docs/user-guide/tasks/build-packages/package-spec.html#package-match-specifications
+# PyQt5 and ase are not available on conda so they are installed via the script above
 requirements:
   build:
     - conda-build
-    - python
+  host:
+    - python =3.8
     - pip
   run:
-    - tornado ==4.5.3
+    - python =3.8
+
     - astropy
-    - xarray ==0.9.6
-    - h5py ==2.7.0
-    - netcdf4
-    - colorcet
-    - colorama
+    - xarray >=0.16.1
+    - h5py >=3.2.1
+    - pyqtgraph >=0.12.0,<0.13.0
+    - pyqt
+
     - pint
     - pandas
-    - dask
-    - numpy
-    - scipy
-    - lmfit
-    - scikit-learn
-    - scikit-image
+    - numpy>=1.20.0,<2.0.0
+    - scipy>=1.6.0,<2.0.0
+    - netcdf4 >=1.5.0,<2.0.0
+    - lmfit >=1.0.0,<2.0.0
+
+    - colorcet
+    - matplotlib >=3.0.3
+    - bokeh >=2.0.0,<3.0.0
+    - ipywidgets >=7.0.1,<8.0.0
+
+    - scikit-learn >=0.24.0,<1.0.0
+
+    - packaging
+    - numba >=0.53.0,<1.0.0
+
+    - colorama
     - imageio
+    - titlecase
 
-    - matplotlib >=3.0.0
-    - bokeh ==0.12.10
-    - xlrd
-    - openpyxl
-    - toolz >=0.7.3
     - tqdm
+    - rx
+    - dill
 
 
-# Optional dependencies
-# - seaborn
-# - PyQt5
-# - pyqtgraph
-# - igor ==0.3.1
-
 test:
   imports:
     - arpes
-
   requires:
     - python
 
 about:
   home: https://arpes.readthedocs.io/
   license: GPL-3.0
   license_family: GPL
+  license_file: LICENSE
   summary: 'Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)'
   description: 'Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)'
   doc_url: https://arpes.readthedocs.io/

docs/source/conf.py

@@ -77,7 +77,7 @@ def setup(app):
     app.connect("autodoc-skip-member", autodoc_skip_member)
 
 
-autodoc_mock_imports = ["torch", "pytorch_lightning", "xrft"]
+autodoc_mock_imports = ["torch", "pytorch_lightning"]
 
 
 # Napoleon settings

environment-readthedocs.yml

@@ -8,22 +8,21 @@ dependencies:
   - astropy
   - xarray>=0.16.1
   - h5py>=3.2.1
-  - pyqtgraph==0.12
+  - pyqtgraph>=0.12.0,<0.13.0
 
   - pint
   - pandas
-  - dask
-  - numpy
-  - scipy
-  - lmfit==1.0
-  - netCDF4
+
+  - numpy>=1.20.0,<2.0.0
+  - scipy>=1.6.0,<2.0.0
+  - lmfit>=1.0.0,<2.0.0
+  - netCDF4>=1.5.0,<2.0.0
 
   # plotting
   - colorcet
   - matplotlib>=3.0.3
-  - seaborn
-  - bokeh>=2.0.0
-  - ipywidgets==7.0.1
+  - bokeh>=2.0.0,<3.0.0
+  - ipywidgets>=7.0.1,<8.0.0
 
   # Misc deps
   - pip
@@ -32,17 +31,16 @@ dependencies:
   - pip:
       - PyQt5==5.15
       - packaging
-      - deprecation
-      - xlrd
-      - numba
+      - numba>=0.53.0,<1.0.0
       - colorama
       - imageio
       - titlecase
-      - openpyxl
       - tqdm
       - rx
       - dill
-      - ase
+      - ase>=3.20.0,<4.0.0
+
+      # documentation dependencies are basically only these
       - sphinx
       - sphinxcontrib-restbuilder
       - sphinx_rtd_theme

environment-update-deploy.yml

@@ -1,6 +1,5 @@
 name: arpes
 channels:
-  - arpes
   - defaults
   - conda-forge
 dependencies:
@@ -9,40 +8,35 @@ dependencies:
   - astropy
   - xarray>=0.16.1
   - h5py>=3.2.1
-  - pyqtgraph==0.12
+  - pyqtgraph>=0.12.0,<0.13.0
 
   - pint
   - pandas
-  - dask
-  - numpy
-  - scipy
-  - lmfit==1.0
-  - netCDF4
+  - numpy>=1.20.0,<2.0.0
+  - scipy>=1.6.0,<2.0.0
+  - lmfit>=1.0.0,<2.0.0
+  - netCDF4>=1.5.0,<2.0.0
 
   # plotting
   - colorcet
   - matplotlib>=3.0.3
-  - seaborn
-  - bokeh>=2.0.0
-  - ipywidgets==7.0.1
+  - bokeh>=2.0.0,<3.0.0
+  - ipywidgets>=7.0.1,<8.0.0
 
   # Misc deps
-  - scikit-learn
+  - scikit-learn>=0.24.0,<1.0.0
   - pip
 
   # pip
   - pip:
       - PyQt5==5.15
       - packaging
-      - deprecation
-      - xlrd
-      - numba
+      - numba>=0.53.0,<1.0.0
       - colorama
       - imageio
       - titlecase
-      - openpyxl
       - tqdm
       - rx
       - dill
-      - ase
+      - ase>=3.20.0,<4.0.0
       - -e .

environment-update-docs.yml

@@ -24,40 +24,36 @@
 DEPENDENCY_GROUPS = {
     "core": [
         "astropy",
-        "xarray",
+        "xarray>=0.16.1",
         "h5py>=3.2.1",
-        "pyqtgraph==0.12",
+        "pyqtgraph>=0.12.0,<0.13.0",
         "PyQt5==5.15",
-        "netCDF4",
+        "netCDF4>=1.5.0,<2.0.0",
         "colorcet",
         "pint",
         "pandas",
-        "dask",
-        "numpy",
-        "scipy",
-        "lmfit==1.0",
+        "numpy>=1.20.0,<2.0.0",
+        "scipy>=1.6.0,<2.0.0",
+        "lmfit>=1.0.0,<2.0.0",
         "scikit-learn",
         # plotting
         "matplotlib>=3.0.3",
-        "seaborn",
-        "bokeh>=2.0.0",
-        "ipywidgets==7.0.1",
+        "bokeh>=2.0.0,<3.0.0",
+        "ipywidgets>=7.0.1,<8.0.0",
         # Misc deps
-        "deprecation",
         "packaging",
-        "xlrd",
         "colorama",
         "imageio",
         "titlecase",
-        "openpyxl",
         "tqdm",
         "rx",
         "dill",
-        "ase",
+        "ase>=3.20.0,<4.0.0",
+        "numba>=0.53.0,<1.0.0",
     ],
     "igor": ["igor==0.3.1"],
     "ml": [
-        "scikit-learn",
+        "scikit-learn>=0.24.0,<1.0.0",
         "scikit-image",
         "cvxpy",
         "libgcc",
@@ -83,7 +79,7 @@
 }
 
 
-with open("pypi-readme.rst", "r") as f_readme:
+with open("./pypi-readme.rst", "r") as f_readme:
     long_description = f_readme.read()
 
 
@@ -114,6 +110,7 @@
         "tests",
         "source",
         "info_session",
+        "scripts",
         "docs",
         "example_configuration",
         "conda",