Merge with Juan's fork.

ITA-Solar · Mar 2, 2023 · 615c26c · 615c26c
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,34 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags:
+      - 'v*'
+      - '!*dev*'
+      - '!*pre*'
+      - '!*post*'
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  core:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    with:
+      submodules: false
+      envs: |
+        - linux: py310
+
+  test:
+    needs: [core]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    with:
+      submodules: false
+      envs: |
+        - windows: py39
+        - macos: py38
diff --git a/.gitignore b/.gitignore
@@ -88,3 +88,15 @@ ENV/
 
 # Rope project settings
 .ropeproject
+
+# VSCode
+.vscode/
+.history/
+
+# Cython Creations
+helita/io/anapyio.c
+helita/sim/cstagger.c
+helita/utils/radtrans.c
+helita/utils/utilsfast.c
+
+*~
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,58 @@
+repos:
+# The warnings/errors we check for here are:
+  # E901 - SyntaxError or IndentationError
+  # E902 - IOError
+  # F822 - undefined name in __all__
+  # F823 - local variable name referenced before assignment
+  # Others are taken care of by autopep8
+  - repo: https://github.com/PyCQA/flake8
+    rev: 5.0.4
+    hooks:
+      - id: flake8
+        args:
+          [
+            "--count",
+            "--select",
+            "E901,E902,F822,F823",
+          ]
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v1.7.7
+    hooks:
+      - id: autoflake
+        args:
+          [
+            "--in-place",
+            "--remove-all-unused-imports",
+            "--remove-unused-variable",
+          ]
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: ["--sp", "setup.cfg"]
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v2.0.0
+    hooks:
+    -   id: autopep8
+        args: ["--in-place","--max-line-length", "200"]
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-ast
+      - id: check-case-conflict
+      - id: trailing-whitespace
+        exclude: ".*(.fits|.fts|.fit|.header|.txt)$"
+      - id: check-yaml
+      - id: debug-statements
+      - id: check-added-large-files
+        args: ['--enforce-all','--maxkb=1054']
+      - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.json)$|^CITATION.rst$"
+      - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+ci:
+  autofix_prs: false
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017, The Helita developers and Institute of Theoretical Astrophysics.
+Copyright (c) 2017-2022, The Helita developers and Institute of Theoretical Astrophysics.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/README.md b/README.md
@@ -1,9 +1,10 @@
 # Helita
 
-Helita is a Python library for solar physics focused on interfacing with code and projects from the [Institute of Theoretical Astrophysics](http://astro.uio.no) (ITA) and the [Rosseland Centre for Solar Physics](https://www.mn.uio.no/rocs/) (RoCS) at the [University of Oslo](https://www.uio.no). The name comes from Helios + ITA.
+Helita is a Python library for solar physics focused on interfacing with code and projects from the [Institute of Theoretical Astrophysics](http://astro.uio.no) (ITA) and the [Rosseland Centre for Solar Physics](https://www.mn.uio.no/rocs/) (RoCS) at the [University of Oslo](https://www.uio.no).
+The name comes from Helios + ITA.
 
 The library is a loose collection of different scripts and classes with varying degrees of portability and usefulness.
 
 ## Documentation
 
-For more details including installation instructions, please see the documentation at http://ita-solar.github.io/helita.
+For more details including installation instructions, [please see the documentation.](http://ita-solar.github.io/helita)
diff --git a/helita/__init__.py b/helita/__init__.py
@@ -4,7 +4,7 @@
 
 __all__ = ["io", "obs", "sim", "utils"]
 
-from . import io
-from . import obs
-from . import sim
-from . import utils
+#from . import io
+#from . import obs
+#from . import sim
+#from . import utils
diff --git a/helita/io/anapyio.pyx b/helita/io/anapyio.pyx
@@ -1,7 +1,11 @@
 import os
+
 import numpy as np
+
 cimport numpy as np
 from stdlib cimport free, malloc
+
+
 cdef extern from "stdlib.h":
      void *memcpy(void *dst, void *src, long n)
 

diff --git a/helita/io/crispex.py b/helita/io/crispex.py
@@ -1,9 +1,9 @@
 """
 set of tools to deal with crispex data
 """
-import xarray
 import numpy as np
 import scipy.interpolate as interp
+import xarray
 
 
 def write_buf(intensity, outfile, wave=None, stokes=False):

diff --git a/helita/io/lp.py b/helita/io/lp.py
@@ -1,9 +1,10 @@
 """
 Set of tools to read and write 'La Palma' cubes
 """
-import numpy as np
 import os
 
+import numpy as np
+
 
 def make_header(image):
     ''' Creates header for La Palma images. '''

diff --git a/helita/io/sdf.py b/helita/io/sdf.py
@@ -11,7 +11,6 @@ def __init__(self, filename, verbose=False):
         self.verbose = verbose
         self.query(filename)
 
-
     def query(self, filename, verbose=False):
         ''' Queries the file, returning datasets and shapes.'''
         f = open(filename, 'r')
@@ -32,7 +31,6 @@ def query(self, filename, verbose=False):
         self.header_data(header)
         return
 
-
     def header_data(self, header):
         ''' Breaks header string into variable informationp. '''
         self.variables = {}

diff --git a/helita/io/src/anacompress.c b/helita/io/src/anacompress.c
@@ -41,7 +41,7 @@ int anacrunchrun8(uint8_t *x,uint8_t *array,int slice,int nx,int ny,int limit,in
  for (iy=0;iy<ny;iy++) {                 	/* start of iy (outer) loop */
  /* load the first value */
  x[i++] = array[iy*nx];
- 
+
  /* compute and store the first differences for this line */
  p = (array+nx*iy);	nc=nx-1;
  d=dif; yq=(int) *p++;	zq=(int) *p++;
@@ -125,7 +125,7 @@ int anacrunchrun8(uint8_t *x,uint8_t *array,int slice,int nx,int ny,int limit,in
 	 else { y.i=(y.i & mask)<<j; x[i]=x[i] | y.b[0];}
     if (nb>1) { x[i+1]=y.b[1]; if (nb>2) x[i+2]=y.b[2]; }
   }
- 
+
  r1=r1+slice;       			/* bump r1 pass the fixed part */
  i=r1>>3;                j=r1 & 7;
  /* note that r3 is the # of bits required minus 1 */
@@ -174,7 +174,7 @@ int anacrunchrun8(uint8_t *x,uint8_t *array,int slice,int nx,int ny,int limit,in
  /* we have to put these in a form readable by the Vax (these may be used
 	 by fcwrite) */
   if(t_endian){ // big endian
-   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1); 
+   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1);
   }
  free(dif);
  return  i;      /*return # of bytes used */
@@ -454,7 +454,7 @@ int anacrunchrun(uint8_t *x,int16_t *array,int slice,int nx,int ny,int limit,int
  /* we have to put these in a form readable by the Vax (these may be used
 	 by fcwrite) */
  if(t_endian){ // big endian
-   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1); 
+   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1);
  }
  free(dif);
  return  i;      /*return # of bytes used */
@@ -464,7 +464,7 @@ int anacrunchrun(uint8_t *x,int16_t *array,int slice,int nx,int ny,int limit,int
 
 int anacrunch(uint8_t *x,int16_t *array,int slice,int nx,int ny,int limit,int t_endian)
 // compress 16 bit array into x (a byte array) using ny blocks each of size
-// nx, bit slice size slice, returns # of bytes in x 
+// nx, bit slice size slice, returns # of bytes in x
  {
   uint8_t bits[8]={1,2,4,8,16,32,64,128};
   unsigned register i,j,r1,in;
@@ -487,9 +487,9 @@ int anacrunch(uint8_t *x,int16_t *array,int slice,int nx,int ny,int limit,int t_
   mask-=1;                                // no inline expon. in C
   unsigned nb;                            // determine the # of bytes to transfer to 32 bit int for fixed portion
   if(slice==0){
-    nb=0; 
+    nb=0;
   }else{
-    if(slice<2){ 
+    if(slice<2){
       nb=1;
     }else{
       if(slice<10) nb=2; else nb=3;
@@ -602,7 +602,7 @@ int anacrunch(uint8_t *x,int16_t *array,int slice,int nx,int ny,int limit,int t_
   if(t_endian){  // we have to put these in a form readable by the Vax (these may be used by fcwrite)
     bswapi32(&(ch->tsize),1);
     bswapi32(&(ch->bsize),1);
-    bswapi32(&(ch->nblocks),1); 
+    bswapi32(&(ch->nblocks),1);
   }
   return i;     // return # of bytes used
 }
@@ -725,9 +725,8 @@ int anacrunch32(uint8_t *x,int32_t *array,int slice,int nx,int ny,int limit,int
  /* we have to put these in a form readable by the Vax (these may be used
 	 by fcwrite) */
  if(t_endian){ // big endian
-   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1); 
+   bswapi32(&(ch->tsize),1); bswapi32(&(ch->bsize),1); bswapi32(&(ch->nblocks),1);
  }
  /* printf("number of big ones for this I*4 = %d\n", big); */
  return  i;      /*return # of bytes used */
  }       /* end of routine */
-