Fix numba warnings

.github/workflows/deploy.yml

@@ -40,8 +40,8 @@ jobs:
           pip install -r requirements.txt
           conda info
           conda list
-      - name: 📦 Installing graphviz
-        uses: ts-graphviz/setup-graphviz@v1
+      # - name: 📦 Installing graphviz
+      #   uses: ts-graphviz/setup-graphviz@v1
       - name: 👀 Check Tensorflow installation
         shell: bash -l {0}
         run: |

conda-linux-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 384d0a802e8a24cddf93e935a2c3f7af35bb866f4082a51164e36617cd6820ae
+# input_hash: e7114246abce88e6e9c004761119055639b9f24706af05cde369526b00c0d3d1
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda#f5c65075fc34438d5b456c7f3f5ab695
@@ -26,6 +26,7 @@ https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda#e
 https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda#418c6ca5929a611cbd69204907a83995
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 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37
+https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h0b41bf4_3.conda#96f3b11872ef6fad973eac856cd2624f
 https://conda.anaconda.org/conda-forge/linux-64/gmp-6.2.1-h58526e2_0.tar.bz2#b94cf2db16066b242ebd26db2facbd56
 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2#8c54672728e8ec6aa6db90cf2806d220
 https://conda.anaconda.org/conda-forge/linux-64/icu-72.1-hcb278e6_0.conda#7c8d20d847bb45f56bd941578fcfa146
@@ -47,6 +48,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libopus-1.3.1-h7f98852_1.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.17-h166bdaf_0.tar.bz2#b7463391cf284065294e2941dd41ab95
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 https://conda.anaconda.org/conda-forge/linux-64/libtasn1-4.19.0-h166bdaf_0.tar.bz2#93840744a8552e9ebf6bb1a5dffc125a
+https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f204c8ba400ec475452737094fb81d52
 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a
 https://conda.anaconda.org/conda-forge/linux-64/libunwind-1.6.2-h9c3ff4c_0.tar.bz2#a730b2badd586580c5752cc73842e068
 https://conda.anaconda.org/conda-forge/linux-64/libutf8proc-2.8.0-h166bdaf_0.tar.bz2#ede4266dc02e875fe1ea77b25dd43747
@@ -102,7 +104,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.b
 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c
 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.11.4-h0d562d8_0.conda#e46fad17d5fb57316b956f88dca765e4
 https://conda.anaconda.org/conda-forge/linux-64/mpfr-4.2.0-hb012696_0.conda#14d87bdff2cbd3b1179a29fb316ed743
-https://conda.anaconda.org/conda-forge/linux-64/mysql-common-8.0.32-hf1915f5_2.conda#cf4a8f520fdad3a63bb2bce74576cd2d
+https://conda.anaconda.org/conda-forge/linux-64/mysql-common-8.0.32-hf1915f5_3.conda#3cbb1d20331e8b1f170de5cef410cd80
 https://conda.anaconda.org/conda-forge/linux-64/openblas-0.3.23-pthreads_h855a84d_0.conda#ba8810202f8879562f01b4f9957c1ada
 https://conda.anaconda.org/conda-forge/linux-64/openblas-ilp64-0.3.23-pthreads_h3d04fff_0.conda#9787e8492f0a51a6b0498dc86f3864f9
 https://conda.anaconda.org/conda-forge/linux-64/openspecfun-0.5.5-hb600da9_1.tar.bz2#10db64a1d68142d26dc6348db7b99cfe
@@ -126,12 +128,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libgit2-1.6.4-h747ad27_0.conda#2
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 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-17_linux64_openblas.conda#a2103882c46492e26500fcb56c03de8b
-https://conda.anaconda.org/conda-forge/linux-64/libllvm16-16.0.5-h5cf9203_0.conda#2d7677652a00dcfaed23acd066fa72a5
+https://conda.anaconda.org/conda-forge/linux-64/libllvm16-16.0.6-h5cf9203_0.conda#753e078cccad40fe4b396bdcf27a3c15
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-https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.0-ha587672_6.conda#4e5ee4b062c21519efbee7e2ae608748
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.1-h8b53f26_0.conda#8ad377fb60abab446a9f02c62b3c2190
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-https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.32-hca2cd23_2.conda#20b4708cd04bdc8138d03314ddd97885
+https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.32-hca2cd23_3.conda#247055daf6d75d72ac0e94de151e8ab0
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 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-hd590300_1.conda#9bfac7ccd94d54fd21a0501296d60424
@@ -142,6 +144,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.5-h8ee46fc_0.con
 https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.13-pyhd8ed1ab_0.conda#06006184e203b61d3525f90de394471e
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 https://conda.anaconda.org/conda-forge/linux-64/arpack-3.7.0-hdefa2d7_2.tar.bz2#8763fe86163198ef1778d1d8d22bb078
+https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-hd4edc92_1.tar.bz2#6c72ec3e660a51736913ef6ea68c454b
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 https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_3.conda#54ca2e08b3220c148a1d8329c2678e02
@@ -167,9 +170,11 @@ https://conda.anaconda.org/conda-forge/noarch/executing-1.2.0-pyhd8ed1ab_0.tar.b
 https://conda.anaconda.org/conda-forge/noarch/filelock-3.12.2-pyhd8ed1ab_0.conda#53522ec72e6adae42bd373ef58357230
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+https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.10-h6b639ba_2.conda#ee8220db21db8094998005990418fe5b
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 https://conda.anaconda.org/conda-forge/linux-64/greenlet-2.0.2-py39h3d6467e_1.conda#bcc2596fee9dccce15c6ae3d475ea013
+https://conda.anaconda.org/conda-forge/linux-64/gts-0.7.6-h977cf35_4.conda#4d8df0b0db060d33c9a702ada998a8fe
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@@ -183,6 +188,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.1.2-h409715c_0.conda#5
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+https://conda.anaconda.org/conda-forge/linux-64/libwebp-1.3.0-hb47c5f0_0.conda#9cfd7ad6e1539ca1ad172083586b3301
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@@ -272,7 +278,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py39he91dace_3.conda
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-https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.0.7-py39h4b4f3f3_0.conda#c5387f3fb1f5b8b71e1c865fc55f4951
+https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.1.0-py39h7633fee_0.conda#54e6f32e448fdc273606011f0940d076
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@@ -287,14 +293,15 @@ https://conda.anaconda.org/conda-forge/noarch/joblib-1.2.0-pyhd8ed1ab_0.tar.bz2#
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+https://conda.anaconda.org/conda-forge/linux-64/libgd-2.3.3-hfa28ad5_6.conda#ef06bee47510a7f5db3c2297a51d6ce2
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+https://conda.anaconda.org/conda-forge/linux-64/numba-0.57.0-py39hb75a051_2.conda#28954bf5c9d6046b4ee67fbf953de78a
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@@ -336,26 +343,30 @@ https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-21.3.0-pyhd8ed1ab_0.ta
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 https://conda.anaconda.org/conda-forge/linux-64/qt-main-5.15.8-h01ceb2d_12.conda#60fd4bdf187f88bac57cdc1a052f2811
 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.15-pyhd8ed1ab_0.conda#27db656619a55d727eaf5a6ece3d2fd6
+https://conda.anaconda.org/conda-forge/linux-64/graphviz-8.0.5-h28d9a01_0.conda#597e2d0e1c6bc2e4457714ff479fe142
 https://conda.anaconda.org/conda-forge/noarch/ipython-8.14.0-pyh41d4057_0.conda#0a0b0d8177c4a209017b356439292db8
 https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.4-pyhd8ed1ab_0.conda#f7aa15f77d29b11caa1df1eb15383c59
 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py39h5c7b992_3.conda#19e30314fe824605750da905febb8ee6

environment.yaml

@@ -4,6 +4,7 @@ name: L96M2lines
 channels:
   - conda-forge
   - defaults
+  - anaconda
 dependencies:
   - python=3.9
   - matplotlib
@@ -24,3 +25,4 @@ dependencies:
   - xarray
   - pysr
   - nomkl
+  - graphviz

notebooks/DA_methods.py

@@ -3,10 +3,10 @@
 Reference: https://www.mdpi.com/2311-5521/5/4/225
 """
 import numpy as np
-from numba import jit
+from numba import njit
 
 
-@jit(nopython=False)
+@njit
 def Lin3dvar(ub, w, H, R, B, opt):
     # The solution of the 3DVAR problem in the linear case requires
     # the solution of a linear system of equations.
@@ -35,7 +35,7 @@ def Lin3dvar(ub, w, H, R, B, opt):
     return ua
 
 
-@jit(nopython=False)
+@njit
 def ens_inflate(posterior, prior, opt, factor):
     inflated = np.zeros(posterior.shape)
     n, N = prior.shape
@@ -55,7 +55,7 @@ def ens_inflate(posterior, prior, opt, factor):
     return inflated
 
 
-@jit(nopython=False)
+@njit
 def EnKF(prior, obs, H, R, B):
     # The analysis step for the (stochastic) ensemble Kalman filter
     # with virtual observations

notebooks/L96_model.py

@@ -5,10 +5,10 @@
 """
 
 import numpy as np
-from numba import jit
+from numba import jit, njit
 
 
-@jit(nopython=False)
+@njit
 def L96_eq1_xdot(X, F, advect=True):
     """
     Calculate the time rate of change for the X variables for the Lorenz '96, equation 1:
@@ -33,7 +33,7 @@ def L96_eq1_xdot(X, F, advect=True):
     return Xdot
 
 
-@jit(nopython=False)
+@njit
 def L96_2t_xdot_ydot(X, Y, F, h, b, c):
     """
     Calculate the time rate of change for the X and Y variables for the Lorenz '96, two time-scale