"Cannot find implementation or library stub for module named" error has been persisten with neovim's lspconfig.

[MKrbm]

Error message Cannot find implementation or library stub for module named "module name" always appears whenever I define custom modules.

The minimum example project structure is like below where my_add function is defined in foo.py and the main.py tries to import the function.

lib1/ ├── init.py └── foo.py main.py

import numpy as np
from lib1 import foo

def test(a: int, b: int) -> int:
    return a + b

test(np.ones(3), np.ones(3))

When I run mypy from command line, I can get the expected result

❯ mypy mypy.py
mypy.py:9: error: Argument 1 to "test" has incompatible type "ndarray[Any, dtype[floating[_6
4Bit]]]"; expected "int"  [arg-type]
mypy.py:9: error: Argument 2 to "test" has incompatible type "ndarray[Any, dtype[floating[_6
4Bit]]]"; expected "int"  [arg-type]
Found 2 errors in 1 file (checked 1 source file)

The configuration of the pylsp in my neovim is like

print("python_folder: " .. python_folder)
print("python_executable: " .. python_executable)
print("pylsp_executable: " .. pylsp_executable)

require("lspconfig").pylsp.setup({
    cmd = { pylsp_executable, "--log-file", "/tmp/pyls.log" },
    filetypes = { "python" },
    settings = {
        pylsp = {
            configurationSources = { "flake8" },
            plugins = {
                -- formatter options
                black = { enabled = false },
                autopep8 = { enabled = true },
                yapf = { enabled = false },
                -- linter options
                flake8 = { enabled = true },
                pyflakes = { enabled = false },
                pycodestyle = { enabled = false },
                -- type checker
                pylsp_mypy = {
                    enabled = true,
                    overrides = {
                        "--python-executable",
                        python_executable
                    }
                },
                mypy = { enabled = false },
                -- auto-completion options
                jedi_completion = { fuzzy = false },
                -- import sorting
                pyls_isort = { enabled = false },
            },
        },
    },
})

I'been suffering from this bug? for half a year. Is there any solution? Thank you !

[Richardk2n]

You likely want a true somewhere in your overrides. (I really should document that better …) However, this is not the issue at hand. Why are you using the python-executable flag? What happens if you use it from the command line as well?

I guess this could be an issue with having multiple environments. Are you running pylsp in a different environment than your default one/the one you use for the command line invocation?

[Susensio]

I'm having this problem as well. I'm using mypy plugin from mason's virtual environment (not the project virtual environment)

The project virual environment is activated, but I don't know how the two environments work together.

[Richardk2n]

@Susensio You might have to set python-executeable to the project env. Does it work on command line?

[adamingas]

I have the same issue. I set the python-executable to vim.env.VIRTUAL_ENV .. "/bin/python/, and it still doesn't work. I also added a true at the end of the overrides list.

Even if i pass a non-existent python-executable, i.e.

overrides = {--python-executable, 'random', true}

I get not errors in the Logs, and mypy keeps giving me the same Cannot find implementation... errors.

[Richardk2n]

@adamingas Does it work on the command line for you?

[adamingas]

Running mypy from the environment it's installed in (a conda environment) with the correct python executable given as argument (the python binary in my project's venv), works as expected.

I also tried importing mypy and running it from an ipython shell, and that works as well.

[Richardk2n]

The pylsp-mypy log should be part of the lsp-server log. Could you please provide that? I would like to know what calls to mypy are made by pylsp-mypy and with what arguments. Also, please provide your config (to check against what is actually passed).

[adamingas]

Cleared logs, opened a python file, cleared sensitive information, and pasted the logs:

[START][2024-09-06 11:58:44] LSP logging initiated
[INFO][2024-09-06 11:58:44] .../vim/lsp/rpc.lua:662 "Starting RPC client"   {  args = { "/Users/u1078811/.local/share/nvim/plugged/copilot.vim/dist/language-server.js", "--stdio" },  cmd = "node",  extra = {    cwd = "/Users/u1078811"  }}
[DEBUG][2024-09-06 11:58:44] .../vim/lsp/rpc.lua:284    "rpc.send"  {  id = 1,  jsonrpc = "2.0",  method = "initialize",  params = {    capabilities = {      textDocument = {        callHierarchy = {          dynamicRegistration = false        },        codeAction = {          codeActionLiteralSupport = {            codeActionKind = {              valueSet = { "", "quickfix", "refactor", "refactor.extract", "refactor.inline", "refactor.rewrite", "source", "source.organizeImports" }            }          },          dataSupport = true,          dynamicRegistration = false,          isPreferredSupport = true,          resolveSupport = {            properties = { "edit" }          }        },        completion = {          completionItem = {            commitCharactersSupport = false,            deprecatedSupport = false,            documentationFormat = { "markdown", "plaintext" },            preselectSupport = false,            snippetSupport = false          },          completionItemKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 }          },          contextSupport = false,          dynamicRegistration = false        },        declaration = {          linkSupport = true        },        definition = {          linkSupport = true        },        documentHighlight = {          dynamicRegistration = false        },        documentSymbol = {          dynamicRegistration = false,          hierarchicalDocumentSymbolSupport = true,          symbolKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }          }        },        hover = {          contentFormat = { "markdown", "plaintext" },          dynamicRegistration = false        },        implementation = {          linkSupport = true        },        publishDiagnostics = {          relatedInformation = true,          tagSupport = {            valueSet = { 1, 2 }          }        },        references = {          dynamicRegistration = false        },        rename = {          dynamicRegistration = false,          prepareSupport = true        },        semanticTokens = {          augmentsSyntaxTokens = true,          dynamicRegistration = false,          formats = { "relative" },          multilineTokenSupport = false,          overlappingTokenSupport = true,          requests = {            full = {              delta = true            },            range = false          },          serverCancelSupport = false,          tokenModifiers = { "declaration", "definition", "readonly", "static", "deprecated", "abstract", "async", "modification", "documentation", "defaultLibrary" },          tokenTypes = { "namespace", "type", "class", "enum", "interface", "struct", "typeParameter", "parameter", "variable", "property", "enumMember", "event", "function", "method", "macro", "keyword", "modifier", "comment", "string", "number", "regexp", "operator", "decorator" }        },        signatureHelp = {          dynamicRegistration = false,          signatureInformation = {            activeParameterSupport = true,            documentationFormat = { "markdown", "plaintext" },            parameterInformation = {              labelOffsetSupport = true            }          }        },        synchronization = {          didSave = true,          dynamicRegistration = false,          willSave = true,          willSaveWaitUntil = true        },        typeDefinition = {          linkSupport = true        }      },      window = {        showDocument = {          support = true        },        showMessage = {          messageActionItem = {            additionalPropertiesSupport = false          }        },        workDoneProgress = true      },      workspace = {        applyEdit = true,        configuration = true,        didChangeWatchedFiles = {          dynamicRegistration = false,          relativePatternSupport = true        },        semanticTokens = {          refreshSupport = true        },        symbol = {          dynamicRegistration = false,          hierarchicalWorkspaceSymbolSupport = true,          symbolKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }          }        },        workspaceEdit = {          resourceOperations = { "rename", "create", "delete" }        },        workspaceFolders = true      }    },    clientInfo = {      name = "Neovim",      version = "0.9.1"    },    initializationOptions = {      editorInfo = {        name = "Neovim",        version = "0.9.1"      },      editorPluginInfo = {        name = "copilot.vim",        version = "1.39.0"      }    },    processId = 44956,    rootPath = vim.NIL,    rootUri = vim.NIL,    trace = "off",    workspaceFolders = vim.NIL  }}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:387    "rpc.receive"   {  id = 1,  jsonrpc = "2.0",  result = {    capabilities = {      executeCommandProvider = {        commands = { "github.copilot.didAcceptCompletionItem", "github.copilot.didAcceptPanelCompletionItem" }      },      inlineCompletionProvider = vim.empty_dict(),      notebookDocumentSync = {        notebookSelector = { {            notebook = "*"          } }      },      textDocumentSync = {        change = 2,        openClose = true      },      workspace = {        workspaceFolders = {          changeNotifications = true,          supported = true        }      }    },    serverInfo = {      name = "GitHub Copilot Language Server",      nodeVersion = "20.5.0",      version = "1.223.0"    }  }}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "initialized",  params = vim.empty_dict()}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "workspace/didChangeConfiguration",  params = {    settings = {      ["github-enterprise"] = {        uri = vim.NIL      },      http = {        proxy = vim.NIL,        proxyStrictSSL = vim.NIL      }    }  }}
[INFO][2024-09-06 11:58:45] .../lua/vim/lsp.lua:1345    "LSP[GitHub Copilot]"   "server_capabilities"   {  server_capabilities = {    executeCommandProvider = {      commands = { "github.copilot.didAcceptCompletionItem", "github.copilot.didAcceptPanelCompletionItem" }    },    inlineCompletionProvider = vim.empty_dict(),    notebookDocumentSync = {      notebookSelector = { {          notebook = "*"        } }    },    textDocumentSync = {      change = 2,      openClose = true    },    workspace = {      workspaceFolders = {        changeNotifications = true,        supported = true      }    }  }}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:387    "rpc.receive"   {  jsonrpc = "2.0",  method = "window/logMessage",  params = {    message = "[lsp] GitHub Copilot Language Server 1.223.0 initialized",    type = 3  }}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:387    "rpc.receive"   {  id = 0,  jsonrpc = "2.0",  method = "workspace/configuration",  params = {    items = { {        section = "http"      }, {        section = "github-enterprise"      }, {        section = "github.copilot"      } }  }}
[INFO][2024-09-06 11:58:45] ...lsp/handlers.lua:539 "[lsp] GitHub Copilot Language Server 1.223.0 initialized"
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:403    "server_request: callback result"   {  result = { {      proxy = vim.NIL,      proxyStrictSSL = vim.NIL    }, {      uri = vim.NIL    }, vim.NIL },  status = true}
[DEBUG][2024-09-06 11:58:45] .../vim/lsp/rpc.lua:284    "rpc.send"  {  id = 0,  jsonrpc = "2.0",  result = { {      proxy = vim.NIL,      proxyStrictSSL = vim.NIL    }, {      uri = vim.NIL    }, vim.NIL }}
[INFO][2024-09-06 11:58:53] .../vim/lsp/rpc.lua:662 "Starting RPC client"   {  args = {},  cmd = "/Users/u1078811/mambaforge/envs/nvim/bin/pylsp",  extra = {    cwd = "/Users/u1078811/projects/llm_cohort_summary"  }}
[DEBUG][2024-09-06 11:58:53] .../vim/lsp/rpc.lua:284    "rpc.send"  {  id = 1,  jsonrpc = "2.0",  method = "initialize",  params = {    capabilities = {      textDocument = {        callHierarchy = {          dynamicRegistration = false        },        codeAction = {          codeActionLiteralSupport = {            codeActionKind = {              valueSet = { "", "quickfix", "refactor", "refactor.extract", "refactor.inline", "refactor.rewrite", "source", "source.organizeImports" }            }          },          dataSupport = true,          dynamicRegistration = false,          isPreferredSupport = true,          resolveSupport = {            properties = { "edit" }          }        },        completion = {          completionItem = {            commitCharactersSupport = true,            deprecatedSupport = true,            documentationFormat = { "markdown", "plaintext" },            insertReplaceSupport = true,            insertTextModeSupport = {              valueSet = { 1, 2 }            },            labelDetailsSupport = true,            preselectSupport = true,            resolveSupport = {              properties = { "documentation", "detail", "additionalTextEdits", "sortText", "filterText", "insertText", "textEdit", "insertTextFormat", "insertTextMode" }            },            snippetSupport = true,            tagSupport = {              valueSet = { 1 }            }          },          completionItemKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 }          },          completionList = {            itemDefaults = { "commitCharacters", "editRange", "insertTextFormat", "insertTextMode", "data" }          },          contextSupport = true,          dynamicRegistration = false,          insertTextMode = 1        },        declaration = {          linkSupport = true        },        definition = {          linkSupport = true        },        documentHighlight = {          dynamicRegistration = false        },        documentSymbol = {          dynamicRegistration = false,          hierarchicalDocumentSymbolSupport = true,          symbolKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }          }        },        hover = {          contentFormat = { "markdown", "plaintext" },          dynamicRegistration = false        },        implementation = {          linkSupport = true        },        publishDiagnostics = {          relatedInformation = true,          tagSupport = {            valueSet = { 1, 2 }          }        },        references = {          dynamicRegistration = false        },        rename = {          dynamicRegistration = false,          prepareSupport = true        },        semanticTokens = {          augmentsSyntaxTokens = true,          dynamicRegistration = false,          formats = { "relative" },          multilineTokenSupport = false,          overlappingTokenSupport = true,          requests = {            full = {              delta = true            },            range = false          },          serverCancelSupport = false,          tokenModifiers = { "declaration", "definition", "readonly", "static", "deprecated", "abstract", "async", "modification", "documentation", "defaultLibrary" },          tokenTypes = { "namespace", "type", "class", "enum", "interface", "struct", "typeParameter", "parameter", "variable", "property", "enumMember", "event", "function", "method", "macro", "keyword", "modifier", "comment", "string", "number", "regexp", "operator", "decorator" }        },        signatureHelp = {          dynamicRegistration = false,          signatureInformation = {            activeParameterSupport = true,            documentationFormat = { "markdown", "plaintext" },            parameterInformation = {              labelOffsetSupport = true            }          }        },        synchronization = {          didSave = true,          dynamicRegistration = false,          willSave = true,          willSaveWaitUntil = true        },        typeDefinition = {          linkSupport = true        }      },      window = {        showDocument = {          support = true        },        showMessage = {          messageActionItem = {            additionalPropertiesSupport = false          }        },        workDoneProgress = true      },      workspace = {        applyEdit = true,        configuration = true,        didChangeWatchedFiles = {          dynamicRegistration = false,          relativePatternSupport = true        },        semanticTokens = {          refreshSupport = true        },        symbol = {          dynamicRegistration = false,          hierarchicalWorkspaceSymbolSupport = true,          symbolKind = {            valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }          }        },        workspaceEdit = {          resourceOperations = { "rename", "create", "delete" }        },        workspaceFolders = true      }    },    clientInfo = {      name = "Neovim",      version = "0.9.1"    },    initializationOptions = vim.empty_dict(),    processId = 44956,    rootPath = "/Users/u1078811/projects/llm_cohort_summary",    rootUri = "file:///Users/u1078811/projects/llm_cohort_summary",    trace = "off",    workspaceFolders = { {        name = "/Users/u1078811/projects/llm_cohort_summary",        uri = "file:///Users/u1078811/projects/llm_cohort_summary"      } }  }}
[DEBUG][2024-09-06 11:58:53] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "textDocument/didOpen",  params = {    textDocument = {      languageId = "python",      text = "import json\nimport os\nimport time\nimport re\nfrom concurrent.futures import ThreadPoolExecutor, as_completed\n\nimport openai\nfrom openai import AzureOpenAI\nimport pandas as pd\nfrom azure.identity import ClientSecretCredential\nfrom dotenv import load_dotenv\nfrom openai import ChatCompletion\nfrom llm_cohort_summary.data_utils import df_to_natural_language\nfrom llm_cohort_summary.formatter import format_text\n\nfrom llm_cohort_summary.templates.template import CHAT_V4\nfrom llm_cohort_summary.templates.prompt import ChatPromptTemplate, ChatCompletionMessageDict\nfrom llm_cohort_summary.exceptions import AzureAuthError, AzureCredentialsError, ParsingError\nfrom llm_cohort_summary.mlops import custom_logging\nfrom llm_cohort_summary.utils import get_logger\nfrom typing import List, Tuple\n\n\n\    uri = "file:///Users/u1078811/projects/llm_cohort_summary/llm_cohort_summary/summarise_II_async_calls_GPI_seperate.py",      version = 0    }  }}
[DEBUG][2024-09-06 11:58:53] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "textDocument/didFocus",  params = {    textDocument = {      uri = "file:///Users/u1078811/projects/llm_cohort_summary/llm_cohort_summary/summarise_II_async_calls_GPI_seperate.py"    }  }}
[DEBUG][2024-09-06 11:58:55] .../vim/lsp/rpc.lua:387    "rpc.receive"   {  id = 1,  jsonrpc = "2.0",  result = {    capabilities = {      codeActionProvider = true,      codeLensProvider = {        resolveProvider = false      },      completionProvider = {        resolveProvider = true,        triggerCharacters = { "." }      },      definitionProvider = true,      documentFormattingProvider = true,      documentHighlightProvider = true,      documentRangeFormattingProvider = true,      documentSymbolProvider = true,      executeCommandProvider = {        commands = {}      },      experimental = vim.empty_dict(),      foldingRangeProvider = true,      hoverProvider = true,      notebookDocumentSync = {        notebookSelector = { {            cells = { {                language = "python"              } }          } }      },      referencesProvider = true,      renameProvider = true,      signatureHelpProvider = {        triggerCharacters = { "(", ",", "=" }      },      textDocumentSync = {        change = 2,        openClose = true,        save = {          includeText = true        }      },      workspace = {        workspaceFolders = {          changeNotifications = true,          supported = true        }      }    },    serverInfo = {      name = "pylsp",      version = "1.10.0"    }  }}
[DEBUG][2024-09-06 11:58:55] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "initialized",  params = vim.empty_dict()}
[INFO][2024-09-06 11:58:55] .../lua/vim/lsp.lua:1345    "LSP[pylsp]"    "server_capabilities"   {  server_capabilities = {    codeActionProvider = true,    codeLensProvider = {      resolveProvider = false    },    completionProvider = {      resolveProvider = true,      triggerCharacters = { "." }    },    definitionProvider = true,    documentFormattingProvider = true,    documentHighlightProvider = true,    documentRangeFormattingProvider = true,    documentSymbolProvider = true,    executeCommandProvider = {      commands = {}    },    experimental = vim.empty_dict(),    foldingRangeProvider = true,    hoverProvider = true,    notebookDocumentSync = {      notebookSelector = { {          cells = { {              language = "python"            } }        } }    },    referencesProvider = true,    renameProvider = true,    signatureHelpProvider = {      triggerCharacters = { "(", ",", "=" }    },    textDocumentSync = {      change = 2,      openClose = true,      save = {        includeText = true      }    },    workspace = {      workspaceFolders = {        changeNotifications = true,        supported = true      }    }  }}
[DEBUG][2024-09-06 11:58:55] .../vim/lsp/rpc.lua:284    "rpc.send"  {  jsonrpc = "2.0",  method = "textDocument/didOpen",  params = {    textDocument = {      languageId = "python",      text = "import json\nimport os\nimport time\nimport re\nfrom concurrent.futures import ThreadPoolExecutor, as_completed\n\nimport openai\nfrom openai import AzureOpenAI\nimport pandas as pd\nfrom azure.identity import ClientSecretCredential\nfrom dotenv import load_dotenv\nfrom openai import ChatCompletion\nfrom llm_cohort_summary.data_utils import df_to_natural_language\nfrom llm_cohort_summary.formatter import format_text\n\nfrom llm_cohort_summary.templates.template import CHAT_V4\nfrom llm_cohort_summary.templates.prompt import ChatPromptTemplate, ChatCompletionMessageDict\nfrom llm_cohort_summary.exceptions import AzureAuthError, AzureCredentialsError, ParsingError\nfrom llm_cohort_summary.mlops import custom_logging\nfrom llm_cohort_summary.utils import get_logger\nfrom typing import List, Tuple\n\n\n\,      uri = "file:///Users/u1078811/projects/llm_cohort_summary/llm_cohort_summary/summarise_II_async_calls_GPI_seperate.py",      version = 0    }  }}
[DEBUG][2024-09-06 11:58:57] .../vim/lsp/rpc.lua:387    "rpc.receive"   {  jsonrpc = "2.0",  method = "textDocument/publishDiagnostics",  params = {    diagnostics = { {        code = "import-not-found",        message = 'Cannot find implementation or library stub for module named "openai"',        range = {          ["end"] = {            character = 1,            line = 6          },          start = {            character = 0,            line = 6          }        },        severity = 1,        source = "mypy"      }, {        code = "import-not-found",        message = 'Cannot find implementation or library stub for module named "azure.identity"',        range = {          ["end"] = {            character = 1,            line = 9          },          start = {            character = 0,            line = 9          }        },        severity = 1,        source = "mypy"      }, {        message = "See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports",        range = {          ["end"] = {            character = 1,            line = 9          },          start = {            character = 0,            line = 9          }        },        severity = 3,        source = "mypy"      }, {        code = "import-not-found",        message = 'Cannot find implementation or library stub for module named "dotenv"',        range = {          ["end"] = {            character = 1,            line = 10          },          start = {            character = 0,            line = 10          }        },        severity = 1,        source = "mypy"      } },    uri = "file:///Users/u1078811/projects/llm_cohort_summary/llm_cohort_summary/summarise_II_async_calls_GPI_seperate.py"  }}

Note that I can't see the pylsp_mypy logs anywhere in the log file.

My lsp config:

local opts = { noremap=true, silent=true }
vim.keymap.set('n', '<space>e', vim.diagnostic.open_float, opts)
vim.keymap.set('n', '[d', vim.diagnostic.goto_prev, opts)
vim.keymap.set('n', ']d', vim.diagnostic.goto_next, opts)
vim.keymap.set('n', '<space>q', vim.diagnostic.setloclist, opts)

vim.lsp.set_log_level("debug")
-- Use an on_attach function to only map the following keys
-- after the language server attaches to the current buffer
local on_attach = function(client, bufnr)
  -- Enable completion triggered by <c-x><c-o>
  vim.api.nvim_buf_set_option(bufnr, 'omnifunc', 'v:lua.vim.lsp.omnifunc')

  -- Mappings.
  -- See `:help vim.lsp.*` for documentation on any of the below functions
  local bufopts = { noremap=true, silent=true, buffer=bufnr }
  vim.keymap.set('n', 'gD', vim.lsp.buf.declaration, bufopts)
  vim.keymap.set('n', 'gd', vim.lsp.buf.definition, bufopts)
  vim.keymap.set('n', 'K', vim.lsp.buf.hover, bufopts)
  vim.keymap.set('n', 'gi', vim.lsp.buf.implementation, bufopts)
  vim.keymap.set('n', '<C-k>', vim.lsp.buf.signature_help, bufopts)
  vim.keymap.set('n', '<space>wa', vim.lsp.buf.add_workspace_folder, bufopts)
  vim.keymap.set('n', '<space>wr', vim.lsp.buf.remove_workspace_folder, bufopts)
  vim.keymap.set('n', '<space>wl', function()
    print(vim.inspect(vim.lsp.buf.list_workspace_folders()))
  end, bufopts)
  vim.keymap.set('n', '<space>D', vim.lsp.buf.type_definition, bufopts)
  vim.keymap.set('n', '<space>rn', vim.lsp.buf.rename, bufopts)
  vim.keymap.set('n', '<space>ca', vim.lsp.buf.code_action, bufopts)
  vim.keymap.set('n', 'gr', vim.lsp.buf.references, bufopts)
  vim.keymap.set('n', '<space>fr', vim.lsp.buf.format, bufopts)
  vim.keymap.set('n', '<space>e', vim.diagnostic.open_float, bufopts)
end

-- Add additional capabilities supported by nvim-cmp
local capabilities = vim.lsp.protocol.make_client_capabilities()
capabilities = require('cmp_nvim_lsp').default_capabilities(capabilities)

local lspconfig = require('lspconfig')

-- Enable some language servers with the additional completion capabilities offered by nvim-cmp
local servers = {  
    -- 'pyright',
    'pylsp'
}
-- for _, lsp in ipairs(servers) do
--   lspconfig[lsp].setup {
--   }
-- end

mypy_config = {enabled = true}
if vim.env.VIRTUAL_ENV ~=nil then
    mypy_config = {enabled = true, overrides= {true, "--python-executable",vim.env.VIRTUAL_ENV .. "/bin/python"}}
end

lspconfig['pylsp'].setup{
    cmd = {string.sub(vim.g.python3_host_prog,0,-7) .. 'pylsp'}, -- {"/Users/u1078811/mambaforge/envs/nvim/bin/pylsp"},
    on_attach = on_attach,
    capabilities = capabilities,
    pylsp = {
        plugins = {
            ruff = {
                enabled = true,
                unsafe_fixes = true,
                formatEnabled = true,
                format = {'I' , 'F'},
                line_length = 90
            },
            jedi = {
                auto_import_modules = {'pandas','numpy'}
            },
            pylsp_mypy = mypy_config
        }
    }
}
-- lspconfig['ltex'].setup{
--     filetypes = { "bib", "gitcommit", "markdown", "org", "plaintex", "rst", "rnoweb", "tex", "pandoc" ,"vimwiki"}
-- }
lspconfig["jsonls"].setup{
    filetypes = { "json" },
    cmd = {'vscode-json-languageserver', '--stdio'},
}

[adamingas]

Just realised my pylsp config was wrong. The pylsp nested table should be under a settings key. so from

lspconfig['pylsp'].setup{
    cmd = {string.sub(vim.g.python3_host_prog,0,-7) .. 'pylsp'}, -- {"/Users/u1078811/mambaforge/envs/nvim/bin/pylsp"},
    on_attach = on_attach,
    capabilities = capabilities,
    pylsp = {
        plugins = {
            ruff = {
                enabled = true,
                unsafe_fixes = true,
                formatEnabled = true,
                format = {'I' , 'F'},
                line_length = 90
            },
            jedi = {
                auto_import_modules = {'pandas','numpy'}
            },
            pylsp_mypy = mypy_config
        }
    }
}

to

lspconfig['pylsp'].setup{
    cmd = {string.sub(vim.g.python3_host_prog,0,-7) .. 'pylsp'}, -- {"/Users/u1078811/mambaforge/envs/nvim/bin/pylsp"},
    on_attach = on_attach,
    capabilities = capabilities,
    settings = {
        pylsp = {
            plugins = {
                ruff = {
                    enabled = true,
                    unsafe_fixes = true,
                    formatEnabled = true,
                    format = {'I' , 'F'},
                    line_length = 90
                },
                jedi = {
                    auto_import_modules = {'pandas','numpy'}
                },
                pylsp_mypy = mypy_config
            }
        }
    }
}

And using this mypy config

mypy_config = {enabled = true}
if vim.env.VIRTUAL_ENV ~=nil then
    mypy_config = {enabled = true, overrides= {true, "--python-executable",vim.env.VIRTUAL_ENV .. "/bin/python"}}
end

Works with the current active venv's python/packages. With that i consider the issue solved for me.